PDB Short entry for 5L1Z HEADER TRANSCRIPTION/RNA 29-JUL-16 5L1Z TITLE TAR COMPLEX WITH HIV-1 TAT-AFF4-P-TEFB COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYCLIN-DEPENDENT KINASE 9; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: C-2K,CELL DIVISION CYCLE 2-LIKE PROTEIN KINASE 4,CELL COMPND 5 DIVISION PROTEIN KINASE 9,SERINE/THREONINE-PROTEIN KINASE PITALRE, COMPND 6 TAT-ASSOCIATED KINASE COMPLEX CATALYTIC SUBUNIT; COMPND 7 EC: 2.7.11.22,2.7.11.23; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: CYCLIN-T1; COMPND 11 CHAIN: B; COMPND 12 SYNONYM: CYCLIN-T; COMPND 13 ENGINEERED: YES; COMPND 14 MOL_ID: 3; COMPND 15 MOLECULE: AF4/FMR2 FAMILY MEMBER 4; COMPND 16 CHAIN: C; COMPND 17 SYNONYM: ALL1-FUSED GENE FROM CHROMOSOME 5Q31 PROTEIN,PROTEIN AF- COMPND 18 5Q31,MAJOR CDK9 ELONGATION FACTOR-ASSOCIATED PROTEIN; COMPND 19 ENGINEERED: YES; COMPND 20 MOL_ID: 4; COMPND 21 MOLECULE: PROTEIN TAT; COMPND 22 CHAIN: D; COMPND 23 SYNONYM: TRANSACTIVATING REGULATORY PROTEIN; COMPND 24 ENGINEERED: YES; COMPND 25 MOL_ID: 5; COMPND 26 MOLECULE: RNA (5'- COMPND 27 R(P*AP*GP*AP*UP*CP*UP*GP*AP*GP*CP*CP*UP*GP*GP*GP*AP*GP*CP*UP*CP*UP*CP COMPND 28 *U)-3'); COMPND 29 CHAIN: N; COMPND 30 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: CDK9, CDC2L4, TAK; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: CCNT1; SOURCE 13 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 15 MOL_ID: 3; SOURCE 16 SYNTHETIC: YES; SOURCE 17 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 18 ORGANISM_COMMON: HUMAN; SOURCE 19 ORGANISM_TAXID: 9606; SOURCE 20 MOL_ID: 4; SOURCE 21 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 GROUP M SOURCE 22 SUBTYPE B (ISOLATE BH10); SOURCE 23 ORGANISM_COMMON: HIV-1; SOURCE 24 ORGANISM_TAXID: 11678; SOURCE 25 STRAIN: ISOLATE BH10; SOURCE 26 GENE: TAT; SOURCE 27 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 28 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 29 MOL_ID: 5; SOURCE 30 SYNTHETIC: YES; SOURCE 31 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; SOURCE 32 ORGANISM_TAXID: 11676 KEYWDS HIV-1 TAR, PROTEIN-RNA COMPLEX, TRANSCRIPTION, PROTEIN KINASE, KEYWDS 2 TRANSCRIPTION-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR U.SCHULZE-GAHMEN,J.HURLEY REVDAT 6 04-OCT-23 5L1Z 1 REMARK REVDAT 5 21-OCT-20 5L1Z 1 REMARK REVDAT 4 25-DEC-19 5L1Z 1 REMARK REVDAT 3 20-SEP-17 5L1Z 1 REMARK REVDAT 2 02-NOV-16 5L1Z 1 JRNL REVDAT 1 26-OCT-16 5L1Z 0 JRNL AUTH U.SCHULZE-GAHMEN,I.ECHEVERRIA,G.STJEPANOVIC,Y.BAI,H.LU, JRNL AUTH 2 D.SCHNEIDMAN-DUHOVNY,J.A.DOUDNA,Q.ZHOU,A.SALI,J.H.HURLEY JRNL TITL INSIGHTS INTO HIV-1 PROVIRAL TRANSCRIPTION FROM INTEGRATIVE JRNL TITL 2 STRUCTURE AND DYNAMICS OF THE TAT:AFF4:P-TEFB:TAR COMPLEX. JRNL REF ELIFE V. 5 2016 JRNL REFN ESSN 2050-084X JRNL PMID 27731797 JRNL DOI 10.7554/ELIFE.15910 REMARK 2 REMARK 2 RESOLUTION. 5.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 5.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 500.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 3595 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.217 REMARK 3 FREE R VALUE : 0.313 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.600 REMARK 3 FREE R VALUE TEST SET COUNT : 347 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 5.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 6.11 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 323 REMARK 3 BIN R VALUE (WORKING SET) : 0.4653 REMARK 3 BIN FREE R VALUE : 0.5555 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 42 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5264 REMARK 3 NUCLEIC ACID ATOMS : 447 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 400.7 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 424.4 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 79.05500 REMARK 3 B22 (A**2) : 79.05500 REMARK 3 B33 (A**2) : -158.11100 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.003 REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 16.339; 15.000 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 25.358; 20.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 22.145; 20.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 32.741; 25.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 308.4 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : CNS_TOPPAR:PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : CNS_TOPPAR:DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 3 : CNS_TOPPAR:WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : CNS_TOPPAR:ION.PARAM REMARK 3 PARAMETER FILE 5 : CNS_TOPPAR:CARBOHYDRATE.PARAM REMARK 3 PARAMETER FILE 6 : CAPPING.PARAM REMARK 3 PARAMETER FILE 7 : TPONEW.PARAM REMARK 3 PARAMETER FILE 8 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 TOPOLOGY FILE 7 : NULL REMARK 3 TOPOLOGY FILE 8 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5L1Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-AUG-16. REMARK 100 THE DEPOSITION ID IS D_1000223070. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-JUN-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.3.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1158 REMARK 200 MONOCHROMATOR : KHOZU DOUBLE FLAT CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4988 REMARK 200 RESOLUTION RANGE HIGH (A) : 5.280 REMARK 200 RESOLUTION RANGE LOW (A) : 500.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.25800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 5.28 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 5.41 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 8.23600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 0.090 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ID 4OGR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 66.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.72 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALLIZED FROM 50 MM TRIS 8.5, 0.2M REMARK 280 AMMACETATE, 6 MM MGCL2, 8% PEG 4K AT 291 DEGREE K, PH 8.5, VAPOR REMARK 280 DIFFUSION, SITTING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 69.16667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 34.58333 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 34.58333 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 69.16667 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: PENTAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, N REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 10050 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29680 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -102.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1230 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7490 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: N REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 311.25000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 LYS A 3 REMARK 465 GLN A 4 REMARK 465 TYR A 5 REMARK 465 ASP A 6 REMARK 465 SER A 7 REMARK 465 GLN A 27 REMARK 465 GLY A 28 REMARK 465 THR A 29 REMARK 465 PHE A 30 REMARK 465 ALA A 89 REMARK 465 SER A 90 REMARK 465 PRO A 91 REMARK 465 TYR A 92 REMARK 465 ASN A 93 REMARK 465 ARG A 94 REMARK 465 CYS A 95 REMARK 465 LYS A 96 REMARK 465 MET B 1 REMARK 465 GLU B 2 REMARK 465 GLY B 3 REMARK 465 GLU B 4 REMARK 465 ARG B 5 REMARK 465 LYS B 6 REMARK 465 GLU B 262 REMARK 465 ALA B 263 REMARK 465 ALA B 264 REMARK 465 SER C 32 REMARK 465 PRO C 33 REMARK 465 LYS D 50 REMARK 465 LYS D 51 REMARK 465 ARG D 52 REMARK 465 ARG D 53 REMARK 465 GLN D 54 REMARK 465 ARG D 55 REMARK 465 ARG D 56 REMARK 465 ARG D 57 REMARK 465 A N 20 REMARK 465 U N 42 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 N2 G N 21 N2 G N 21 4558 2.02 REMARK 500 CD2 LEU A 261 CD2 LEU A 261 4557 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 CYS A 10 63.49 -176.32 REMARK 500 PHE A 12 46.46 -96.92 REMARK 500 CYS A 13 79.90 -175.72 REMARK 500 LYS A 40 -61.15 -95.57 REMARK 500 MET A 52 43.02 -90.91 REMARK 500 ASN A 54 71.41 -101.08 REMARK 500 GLU A 55 31.22 -78.32 REMARK 500 PHE A 105 138.46 -37.39 REMARK 500 ASP A 149 45.90 -179.40 REMARK 500 THR A 158 174.87 -56.86 REMARK 500 ASP A 167 75.76 59.30 REMARK 500 LEU A 176 37.94 -90.56 REMARK 500 ALA A 177 102.36 22.07 REMARK 500 LYS A 178 57.13 -65.82 REMARK 500 SER A 180 -149.13 -139.73 REMARK 500 PRO A 182 173.33 -53.51 REMARK 500 VAL A 190 143.58 64.74 REMARK 500 ASP A 205 51.65 -102.95 REMARK 500 SER A 226 145.43 -172.58 REMARK 500 TYR A 282 -66.05 -98.68 REMARK 500 ARG A 284 -59.12 72.85 REMARK 500 ASP A 323 170.77 -53.65 REMARK 500 TRP B 12 33.98 -90.58 REMARK 500 ASP B 30 139.90 -38.37 REMARK 500 GLU B 95 32.47 -91.97 REMARK 500 GLN B 97 59.62 -146.75 REMARK 500 THR B 121 3.96 -65.18 REMARK 500 GLN B 190 -50.28 -124.02 REMARK 500 PRO B 213 177.52 -55.90 REMARK 500 SER B 215 156.26 -47.80 REMARK 500 ALA B 260 -152.87 -70.56 REMARK 500 PRO C 38 158.93 -43.90 REMARK 500 SER C 43 87.69 58.99 REMARK 500 LYS C 44 102.85 -58.73 REMARK 500 TYR C 59 -79.29 -49.18 REMARK 500 ASP C 60 -37.30 -30.18 REMARK 500 ASP C 64 17.49 -65.65 REMARK 500 CYS D 22 99.06 -47.78 REMARK 500 THR D 23 172.15 -55.33 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN D 102 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 261 SG REMARK 620 2 CYS D 25 SG 102.0 REMARK 620 3 CYS D 27 SG 108.7 86.3 REMARK 620 4 CYS D 30 SG 145.3 112.7 73.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN D 101 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS D 22 SG REMARK 620 2 CYS D 34 SG 105.0 REMARK 620 3 CYS D 37 SG 133.6 89.1 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN D 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN D 102 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4OGR RELATED DB: PDB DBREF 5L1Z A 1 330 UNP P50750 CDK9_HUMAN 1 330 DBREF 5L1Z B 1 264 UNP O60563 CCNT1_HUMAN 1 264 DBREF 5L1Z C 32 67 UNP Q9UHB7 AFF4_HUMAN 32 67 DBREF 5L1Z D 1 57 UNP P69697 TAT_HV1B1 1 57 DBREF 5L1Z N 20 42 PDB 5L1Z 5L1Z 20 42 SEQADV 5L1Z ACE D 0 UNP P69697 ACETYLATION SEQRES 1 A 330 MET ALA LYS GLN TYR ASP SER VAL GLU CYS PRO PHE CYS SEQRES 2 A 330 ASP GLU VAL SER LYS TYR GLU LYS LEU ALA LYS ILE GLY SEQRES 3 A 330 GLN GLY THR PHE GLY GLU VAL PHE LYS ALA ARG HIS ARG SEQRES 4 A 330 LYS THR GLY GLN LYS VAL ALA LEU LYS LYS VAL LEU MET SEQRES 5 A 330 GLU ASN GLU LYS GLU GLY PHE PRO ILE THR ALA LEU ARG SEQRES 6 A 330 GLU ILE LYS ILE LEU GLN LEU LEU LYS HIS GLU ASN VAL SEQRES 7 A 330 VAL ASN LEU ILE GLU ILE CYS ARG THR LYS ALA SER PRO SEQRES 8 A 330 TYR ASN ARG CYS LYS GLY SER ILE TYR LEU VAL PHE ASP SEQRES 9 A 330 PHE CYS GLU HIS ASP LEU ALA GLY LEU LEU SER ASN VAL SEQRES 10 A 330 LEU VAL LYS PHE THR LEU SER GLU ILE LYS ARG VAL MET SEQRES 11 A 330 GLN MET LEU LEU ASN GLY LEU TYR TYR ILE HIS ARG ASN SEQRES 12 A 330 LYS ILE LEU HIS ARG ASP MET LYS ALA ALA ASN VAL LEU SEQRES 13 A 330 ILE THR ARG ASP GLY VAL LEU LYS LEU ALA ASP PHE GLY SEQRES 14 A 330 LEU ALA ARG ALA PHE SER LEU ALA LYS ASN SER GLN PRO SEQRES 15 A 330 ASN ARG TYR TPO ASN ARG VAL VAL THR LEU TRP TYR ARG SEQRES 16 A 330 PRO PRO GLU LEU LEU LEU GLY GLU ARG ASP TYR GLY PRO SEQRES 17 A 330 PRO ILE ASP LEU TRP GLY ALA GLY CYS ILE MET ALA GLU SEQRES 18 A 330 MET TRP THR ARG SER PRO ILE MET GLN GLY ASN THR GLU SEQRES 19 A 330 GLN HIS GLN LEU ALA LEU ILE SER GLN LEU CYS GLY SER SEQRES 20 A 330 ILE THR PRO GLU VAL TRP PRO ASN VAL ASP ASN TYR GLU SEQRES 21 A 330 LEU TYR GLU LYS LEU GLU LEU VAL LYS GLY GLN LYS ARG SEQRES 22 A 330 LYS VAL LYS ASP ARG LEU LYS ALA TYR VAL ARG ASP PRO SEQRES 23 A 330 TYR ALA LEU ASP LEU ILE ASP LYS LEU LEU VAL LEU ASP SEQRES 24 A 330 PRO ALA GLN ARG ILE ASP SER ASP ASP ALA LEU ASN HIS SEQRES 25 A 330 ASP PHE PHE TRP SER ASP PRO MET PRO SER ASP LEU LYS SEQRES 26 A 330 GLY MET LEU SER THR SEQRES 1 B 264 MET GLU GLY GLU ARG LYS ASN ASN ASN LYS ARG TRP TYR SEQRES 2 B 264 PHE THR ARG GLU GLN LEU GLU ASN SER PRO SER ARG ARG SEQRES 3 B 264 PHE GLY VAL ASP PRO ASP LYS GLU LEU SER TYR ARG GLN SEQRES 4 B 264 GLN ALA ALA ASN LEU LEU GLN ASP MET GLY GLN ARG LEU SEQRES 5 B 264 ASN VAL SER GLN LEU THR ILE ASN THR ALA ILE VAL TYR SEQRES 6 B 264 MET HIS ARG PHE TYR MET ILE GLN SER PHE THR GLN PHE SEQRES 7 B 264 PRO GLY ASN SER VAL ALA PRO ALA ALA LEU PHE LEU ALA SEQRES 8 B 264 ALA LYS VAL GLU GLU GLN PRO LYS LYS LEU GLU HIS VAL SEQRES 9 B 264 ILE LYS VAL ALA HIS THR CYS LEU HIS PRO GLN GLU SER SEQRES 10 B 264 LEU PRO ASP THR ARG SER GLU ALA TYR LEU GLN GLN VAL SEQRES 11 B 264 GLN ASP LEU VAL ILE LEU GLU SER ILE ILE LEU GLN THR SEQRES 12 B 264 LEU GLY PHE GLU LEU THR ILE ASP HIS PRO HIS THR HIS SEQRES 13 B 264 VAL VAL LYS CYS THR GLN LEU VAL ARG ALA SER LYS ASP SEQRES 14 B 264 LEU ALA GLN THR SER TYR PHE MET ALA THR ASN SER LEU SEQRES 15 B 264 HIS LEU THR THR PHE SER LEU GLN TYR THR PRO PRO VAL SEQRES 16 B 264 VAL ALA CYS VAL CYS ILE HIS LEU ALA CYS LYS TRP SER SEQRES 17 B 264 ASN TRP GLU ILE PRO VAL SER THR ASP GLY LYS HIS TRP SEQRES 18 B 264 TRP GLU TYR VAL ASP ALA THR VAL THR LEU GLU LEU LEU SEQRES 19 B 264 ASP GLU LEU THR HIS GLU PHE LEU GLN ILE LEU GLU LYS SEQRES 20 B 264 THR PRO ASN ARG LEU LYS ARG ILE TRP ASN TRP ARG ALA SEQRES 21 B 264 CYS GLU ALA ALA SEQRES 1 C 36 SER PRO LEU PHE ALA GLU PRO TYR LYS VAL THR SER LYS SEQRES 2 C 36 GLU ASP LYS LEU SER SER ARG ILE GLN SER MET LEU GLY SEQRES 3 C 36 ASN TYR ASP GLU MET LYS ASP PHE ILE GLY SEQRES 1 D 58 ACE MET GLU PRO VAL ASP PRO ARG LEU GLU PRO TRP LYS SEQRES 2 D 58 HIS PRO GLY SER GLN PRO LYS THR ALA CYS THR ASN CYS SEQRES 3 D 58 TYR CYS LYS LYS CYS CYS PHE HIS CYS GLN VAL CYS PHE SEQRES 4 D 58 ILE THR LYS ALA LEU GLY ILE SER TYR GLY ARG LYS LYS SEQRES 5 D 58 ARG ARG GLN ARG ARG ARG SEQRES 1 N 23 A G A U C U G A G C C U G SEQRES 2 N 23 G G A G C U C U C U MODRES 5L1Z TPO A 186 THR MODIFIED RESIDUE HET TPO A 186 11 HET ACE D 0 3 HET ZN D 101 1 HET ZN D 102 1 HETNAM TPO PHOSPHOTHREONINE HETNAM ACE ACETYL GROUP HETNAM ZN ZINC ION HETSYN TPO PHOSPHONOTHREONINE FORMUL 1 TPO C4 H10 N O6 P FORMUL 4 ACE C2 H4 O FORMUL 6 ZN 2(ZN 2+) HELIX 1 AA1 GLU A 15 SER A 17 5 3 HELIX 2 AA2 PRO A 60 GLN A 71 1 12 HELIX 3 AA3 LEU A 110 ASN A 116 1 7 HELIX 4 AA4 THR A 122 ASN A 143 1 22 HELIX 5 AA5 THR A 191 ARG A 195 5 5 HELIX 6 AA6 PRO A 196 LEU A 201 1 6 HELIX 7 AA7 PRO A 208 ARG A 225 1 18 HELIX 8 AA8 THR A 233 CYS A 245 1 13 HELIX 9 AA9 ASN A 255 TYR A 259 5 5 HELIX 10 AB1 LYS A 274 LEU A 279 1 6 HELIX 11 AB2 LEU A 279 ARG A 284 1 6 HELIX 12 AB3 ASP A 285 LEU A 296 1 12 HELIX 13 AB4 ASP A 305 ASN A 311 1 7 HELIX 14 AB5 HIS A 312 TRP A 316 5 5 HELIX 15 AB6 LEU A 324 SER A 329 1 6 HELIX 16 AB7 ASN B 9 TYR B 13 5 5 HELIX 17 AB8 THR B 15 ASN B 21 1 7 HELIX 18 AB9 SER B 22 PHE B 27 5 6 HELIX 19 AC1 ASP B 30 LEU B 52 1 23 HELIX 20 AC2 SER B 55 TYR B 70 1 16 HELIX 21 AC3 PRO B 79 GLU B 95 1 17 HELIX 22 AC4 LYS B 100 HIS B 113 1 14 HELIX 23 AC5 SER B 123 LEU B 144 1 22 HELIX 24 AC6 HIS B 152 VAL B 164 1 13 HELIX 25 AC7 SER B 167 LEU B 184 1 18 HELIX 26 AC8 THR B 186 GLN B 190 5 5 HELIX 27 AC9 THR B 192 ASN B 209 1 18 HELIX 28 AD1 HIS B 220 VAL B 225 5 6 HELIX 29 AD2 THR B 230 GLU B 246 1 17 HELIX 30 AD3 ASP C 46 SER C 54 1 9 HELIX 31 AD4 TYR C 59 LYS C 63 5 5 HELIX 32 AD5 GLU D 9 HIS D 13 5 5 HELIX 33 AD6 LYS D 29 HIS D 33 5 5 HELIX 34 AD7 CYS D 34 LYS D 41 1 8 SHEET 1 AA1 5 TYR A 19 ILE A 25 0 SHEET 2 AA1 5 VAL A 33 HIS A 38 -1 O VAL A 33 N ILE A 25 SHEET 3 AA1 5 LYS A 44 LYS A 49 -1 O VAL A 45 N ALA A 36 SHEET 4 AA1 5 ILE A 99 ASP A 104 -1 O PHE A 103 N ALA A 46 SHEET 5 AA1 5 LEU A 81 ARG A 86 -1 N GLU A 83 O VAL A 102 SHEET 1 AA2 3 HIS A 108 ASP A 109 0 SHEET 2 AA2 3 VAL A 155 ILE A 157 -1 O ILE A 157 N HIS A 108 SHEET 3 AA2 3 LEU A 163 LEU A 165 -1 O LYS A 164 N LEU A 156 SHEET 1 AA3 2 TRP B 210 GLU B 211 0 SHEET 2 AA3 2 TYR C 39 LYS C 40 -1 O TYR C 39 N GLU B 211 LINK C TYR A 185 N TPO A 186 1555 1555 1.33 LINK C TPO A 186 N ASN A 187 1555 1555 1.33 LINK C ACE D 0 N MET D 1 1555 1555 1.33 LINK SG CYS B 261 ZN ZN D 102 1555 1555 2.62 LINK SG CYS D 22 ZN ZN D 101 1555 1555 2.60 LINK SG CYS D 25 ZN ZN D 102 1555 1555 2.44 LINK SG CYS D 27 ZN ZN D 102 1555 1555 2.61 LINK SG CYS D 30 ZN ZN D 102 1555 1555 2.73 LINK SG CYS D 34 ZN ZN D 101 1555 1555 2.39 LINK SG CYS D 37 ZN ZN D 101 1555 1555 2.38 CISPEP 1 ASP A 318 PRO A 319 0 -0.03 SITE 1 AC1 4 CYS D 22 HIS D 33 CYS D 34 CYS D 37 SITE 1 AC2 4 CYS B 261 CYS D 25 CYS D 27 CYS D 30 CRYST1 146.870 146.870 103.750 90.00 90.00 120.00 P 32 2 1 6 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.006809 0.003931 0.000000 0.00000 SCALE2 0.000000 0.007862 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009639 0.00000