PDB Short entry for 1WH8 HEADER TRANSCRIPTION 28-MAY-04 1WH8 TITLE SOLUTION STRUCTURE OF THE THIRD CUT DOMAIN OF HUMAN HOMEOBOX PROTEIN TITLE 2 CUX-2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HOMEOBOX PROTEIN CUX-2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CUT DOMAIN; COMPND 5 SYNONYM: CUT-LIKE 2; COMPND 6 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: KAZUSA CDNA HG03205; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: P040114-59; SOURCE 8 OTHER_DETAILS: CELL-FREE PROTEIN SYNTHESIS KEYWDS CUT DOMAIN, STRUCTURAL GENOMICS, RIKEN STRUCTURAL GENOMICS/PROTEOMICS KEYWDS 2 INITIATIVE, RSGI, TRANSCRIPTION EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR N.NAMEKI,N.TOCHIO,S.KOSHIBA,T.KIGAWA,S.YOKOYAMA,RIKEN STRUCTURAL AUTHOR 2 GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 3 02-MAR-22 1WH8 1 REMARK SEQADV REVDAT 2 24-FEB-09 1WH8 1 VERSN REVDAT 1 28-NOV-04 1WH8 0 JRNL AUTH N.NAMEKI,N.TOCHIO,S.KOSHIBA,T.KIGAWA,S.YOKOYAMA JRNL TITL SOLUTION STRUCTURE OF THE THIRD CUT DOMAIN OF HUMAN HOMEOBOX JRNL TITL 2 PROTEIN CUX-2 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 3.5, OPALP REMARK 3 AUTHORS : BRUKER (XWINNMR), KORADI, R.,BILLETER, REMARK 3 M.,GUENTERT, P. (OPALP) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1WH8 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-JUN-04. REMARK 100 THE DEPOSITION ID IS D_1000023578. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 120 MM REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.1MM CUT DOMAIN U-15N, 13C; REMARK 210 20MM D-TRIS-HCL(PH 7.0); 100MM REMARK 210 NACL; 1MM D-DTT; 0.02% NAN3; 90% REMARK 210 H2O, 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C REMARK 210 -SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 20020425, NMRVIEW 5.0.4, REMARK 210 KUJIRA 0.901, CYANA 1.0.7 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS, REMARK 210 RESTRAINED MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS, STRUCTURES REMARK 210 WITH THE LOWEST ENERGY, TARGET REMARK 210 FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. REMARK 300 REMARK 300 BIOMOLECULE: 1 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 1 ARG A 35 CD - NE - CZ ANGL. DEV. = 9.7 DEGREES REMARK 500 1 ARG A 35 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 ARG A 35 NE - CZ - NH2 ANGL. DEV. = -4.0 DEGREES REMARK 500 1 ARG A 80 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 9 ARG A 80 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 10 ARG A 80 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 11 ARG A 80 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 15 ARG A 80 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 19 ARG A 80 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 19 ARG A 80 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 19 ARG A 85 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES 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 1 ASP A 28 97.77 -53.97 REMARK 500 1 LYS A 104 -134.16 33.36 REMARK 500 1 SER A 110 -170.04 53.15 REMARK 500 2 ASP A 28 97.53 -62.35 REMARK 500 2 ASN A 44 72.56 43.79 REMARK 500 2 SER A 76 -169.96 -78.41 REMARK 500 2 LYS A 104 -135.96 36.33 REMARK 500 2 LEU A 105 73.65 33.08 REMARK 500 3 ALA A 13 -173.55 53.81 REMARK 500 3 PRO A 14 49.16 -89.34 REMARK 500 3 GLU A 52 -65.46 -93.98 REMARK 500 3 LEU A 55 -77.75 -89.19 REMARK 500 3 SER A 106 -46.92 -138.93 REMARK 500 3 SER A 110 -38.64 -173.41 REMARK 500 4 ILE A 17 -38.74 -151.26 REMARK 500 4 PRO A 25 173.14 -59.98 REMARK 500 4 LEU A 105 11.74 55.33 REMARK 500 5 SER A 9 -162.29 50.73 REMARK 500 5 GLU A 26 93.75 -63.47 REMARK 500 5 LYS A 104 167.04 51.15 REMARK 500 5 LEU A 105 84.77 44.71 REMARK 500 5 SER A 106 -19.69 -153.24 REMARK 500 5 SER A 110 -170.54 58.18 REMARK 500 6 SER A 5 95.39 -174.50 REMARK 500 6 SER A 9 -85.60 -96.68 REMARK 500 6 GLN A 12 105.99 64.49 REMARK 500 6 ASN A 44 81.12 42.06 REMARK 500 6 ARG A 68 57.16 -141.94 REMARK 500 6 SER A 106 -28.41 -158.42 REMARK 500 6 SER A 110 -162.96 58.72 REMARK 500 7 SER A 5 88.37 -158.79 REMARK 500 7 SER A 9 77.98 -159.31 REMARK 500 7 GLN A 12 93.28 -54.17 REMARK 500 7 GLU A 26 104.64 -56.55 REMARK 500 7 ASP A 28 92.01 -67.47 REMARK 500 7 GLU A 52 -63.41 -92.18 REMARK 500 7 LEU A 55 -70.48 -86.69 REMARK 500 7 SER A 76 -173.90 -69.01 REMARK 500 7 LYS A 104 -155.81 41.73 REMARK 500 7 SER A 110 -155.28 50.12 REMARK 500 8 SER A 3 -167.92 58.91 REMARK 500 8 SER A 11 160.26 75.08 REMARK 500 8 GLU A 26 97.43 -66.82 REMARK 500 8 ASN A 44 19.98 58.71 REMARK 500 9 SER A 11 166.32 65.42 REMARK 500 9 GLN A 12 -54.22 -151.68 REMARK 500 9 ALA A 13 155.49 65.85 REMARK 500 9 ASP A 28 89.24 -67.56 REMARK 500 9 LYS A 104 -156.71 33.77 REMARK 500 9 PRO A 108 38.66 -82.38 REMARK 500 REMARK 500 THIS ENTRY HAS 115 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 SER A 6 GLY A 7 5 149.11 REMARK 500 SER A 110 GLY A 111 5 -147.59 REMARK 500 PRO A 108 SER A 109 6 149.46 REMARK 500 SER A 109 SER A 110 10 132.72 REMARK 500 GLY A 1 SER A 2 15 -141.56 REMARK 500 SER A 110 GLY A 111 15 141.72 REMARK 500 SER A 110 GLY A 111 18 133.33 REMARK 500 SER A 109 SER A 110 20 -146.12 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 TYR A 30 0.07 SIDE CHAIN REMARK 500 3 ARG A 48 0.08 SIDE CHAIN REMARK 500 4 ARG A 85 0.14 SIDE CHAIN REMARK 500 5 ARG A 85 0.13 SIDE CHAIN REMARK 500 6 TYR A 8 0.08 SIDE CHAIN REMARK 500 7 ARG A 68 0.09 SIDE CHAIN REMARK 500 7 ARG A 85 0.08 SIDE CHAIN REMARK 500 9 TYR A 30 0.09 SIDE CHAIN REMARK 500 9 ARG A 48 0.09 SIDE CHAIN REMARK 500 10 TYR A 30 0.08 SIDE CHAIN REMARK 500 10 HIS A 94 0.09 SIDE CHAIN REMARK 500 11 ARG A 100 0.09 SIDE CHAIN REMARK 500 13 ARG A 48 0.09 SIDE CHAIN REMARK 500 15 ARG A 35 0.08 SIDE CHAIN REMARK 500 15 HIS A 73 0.10 SIDE CHAIN REMARK 500 17 ARG A 85 0.08 SIDE CHAIN REMARK 500 18 TYR A 8 0.07 SIDE CHAIN REMARK 500 18 ARG A 35 0.09 SIDE CHAIN REMARK 500 19 ARG A 68 0.08 SIDE CHAIN REMARK 500 20 ARG A 35 0.10 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: HSK002100285.2 RELATED DB: TARGETDB DBREF 1WH8 A 8 105 UNP O14529 CUTL2_HUMAN 1047 1144 SEQADV 1WH8 GLY A 1 UNP O14529 CLONING ARTIFACT SEQADV 1WH8 SER A 2 UNP O14529 CLONING ARTIFACT SEQADV 1WH8 SER A 3 UNP O14529 CLONING ARTIFACT SEQADV 1WH8 GLY A 4 UNP O14529 CLONING ARTIFACT SEQADV 1WH8 SER A 5 UNP O14529 CLONING ARTIFACT SEQADV 1WH8 SER A 6 UNP O14529 CLONING ARTIFACT SEQADV 1WH8 GLY A 7 UNP O14529 CLONING ARTIFACT SEQADV 1WH8 SER A 106 UNP O14529 CLONING ARTIFACT SEQADV 1WH8 GLY A 107 UNP O14529 CLONING ARTIFACT SEQADV 1WH8 PRO A 108 UNP O14529 CLONING ARTIFACT SEQADV 1WH8 SER A 109 UNP O14529 CLONING ARTIFACT SEQADV 1WH8 SER A 110 UNP O14529 CLONING ARTIFACT SEQADV 1WH8 GLY A 111 UNP O14529 CLONING ARTIFACT SEQRES 1 A 111 GLY SER SER GLY SER SER GLY TYR SER GLY SER GLN ALA SEQRES 2 A 111 PRO GLY GLY ILE GLN GLU ILE VAL ALA MET SER PRO GLU SEQRES 3 A 111 LEU ASP THR TYR SER ILE THR LYS ARG VAL LYS GLU VAL SEQRES 4 A 111 LEU THR ASP ASN ASN LEU GLY GLN ARG LEU PHE GLY GLU SEQRES 5 A 111 SER ILE LEU GLY LEU THR GLN GLY SER VAL SER ASP LEU SEQRES 6 A 111 LEU SER ARG PRO LYS PRO TRP HIS LYS LEU SER LEU LYS SEQRES 7 A 111 GLY ARG GLU PRO PHE VAL ARG MET GLN LEU TRP LEU ASN SEQRES 8 A 111 ASP PRO HIS ASN VAL GLU LYS LEU ARG ASP MET LYS LYS SEQRES 9 A 111 LEU SER GLY PRO SER SER GLY HELIX 1 1 GLY A 16 SER A 24 1 9 HELIX 2 2 ASP A 28 ASN A 43 1 16 HELIX 3 3 GLY A 46 ILE A 54 1 9 HELIX 4 4 THR A 58 ARG A 68 1 11 HELIX 5 5 SER A 76 ASP A 92 1 17 HELIX 6 6 HIS A 94 LYS A 104 1 11 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000