PDB Short entry for 1HOM HEADER DNA BINDING PROTEIN 08-OCT-91 1HOM TITLE DETERMINATION OF THE THREE-DIMENSIONAL STRUCTURE OF THE ANTENNAPEDIA TITLE 2 HOMEODOMAIN FROM DROSOPHILA IN SOLUTION BY 1H NUCLEAR MAGNETIC TITLE 3 RESONANCE SPECTROSCOPY COMPND MOL_ID: 1; COMPND 2 MOLECULE: ANTENNAPEDIA PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DROSOPHILA MELANOGASTER; SOURCE 3 ORGANISM_COMMON: FRUIT FLY; SOURCE 4 ORGANISM_TAXID: 7227; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DNA-BINDING PROTEIN, DNA BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 19 AUTHOR Y.-Q.QIAN,M.BILLETER,G.OTTING,M.MULLER,W.J.GEHRING,K.WUTHRICH REVDAT 4 23-FEB-22 1HOM 1 KEYWDS REMARK REVDAT 3 24-FEB-09 1HOM 1 VERSN REVDAT 2 01-APR-03 1HOM 1 JRNL REVDAT 1 31-OCT-93 1HOM 0 JRNL AUTH M.BILLETER,Y.QIAN,G.OTTING,M.MULLER,W.J.GEHRING,K.WUTHRICH JRNL TITL DETERMINATION OF THE THREE-DIMENSIONAL STRUCTURE OF THE JRNL TITL 2 ANTENNAPEDIA HOMEODOMAIN FROM DROSOPHILA IN SOLUTION BY 1H JRNL TITL 3 NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY. JRNL REF J.MOL.BIOL. V. 214 183 1990 JRNL REFN ISSN 0022-2836 JRNL PMID 2164583 JRNL DOI 10.1016/0022-2836(90)90155-F REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH Y.Q.QIAN,M.BILLETER,G.OTTING,M.MUELLER,W.J.GEHRING, REMARK 1 AUTH 2 K.WUTHRICH REMARK 1 TITL THE STRUCTURE OF THE ANTENNAPEDIA HOMEODOMAIN DETERMINED BY REMARK 1 TITL 2 NMR SPECTROSCOPY IN SOLUTION: COMPARISON WITH PROKARYOTIC REMARK 1 TITL 3 REPRESSORS REMARK 1 REF CELL(CAMBRIDGE,MASS.) V. 59 573 1989 REMARK 1 REFN ISSN 0092-8674 REMARK 1 REFERENCE 2 REMARK 1 AUTH G.OTTING,Y.-Q.QIAN,M.MUELLER,M.AFFOLTER,W.J.GEHRING, REMARK 1 AUTH 2 K.WUTHRICH REMARK 1 TITL SECONDARY STRUCTURE DETERMINATION FOR THE ANTENNAPEDIA REMARK 1 TITL 2 HOMEODOMAIN BY NUCLEAR MAGNETIC RESONANCE AND EVIDENCE FOR A REMARK 1 TITL 3 HELIX-TURN-HELIX MOTIF REMARK 1 REF EMBO J. V. 7 4305 1988 REMARK 1 REFN ISSN 0261-4189 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DISMAN, AMBER 3.0 REMARK 3 AUTHORS : BRAUN,GO (DISMAN), SINGH,WEINER,CALDWELL,KOLLMAN REMARK 3 (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1HOM COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000173942. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : NULL REMARK 210 PH : NULL REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL REMARK 210 SPECTROMETER FIELD STRENGTH : NULL REMARK 210 SPECTROMETER MODEL : NULL REMARK 210 SPECTROMETER MANUFACTURER : NULL REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : NULL REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 19 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL 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: 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 5 ARG A 10 NE - CZ - NH1 ANGL. DEV. = 5.0 DEGREES REMARK 500 5 ARG A 28 NE - CZ - NH2 ANGL. DEV. = 3.3 DEGREES REMARK 500 6 ARG A 24 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 6 ARG A 29 CD - NE - CZ ANGL. DEV. = 9.4 DEGREES REMARK 500 12 ARG A 28 CD - NE - CZ ANGL. DEV. = 9.3 DEGREES REMARK 500 15 ARG A 10 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 15 ARG A 10 NE - CZ - NH2 ANGL. DEV. = -5.7 DEGREES REMARK 500 16 ARG A 52 CD - NE - CZ ANGL. DEV. = 15.4 DEGREES REMARK 500 16 ARG A 52 NE - CZ - NH1 ANGL. DEV. = 4.6 DEGREES REMARK 500 16 ARG A 52 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 17 ARG A 31 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 19 ARG A 31 NE - CZ - NH2 ANGL. DEV. = -3.2 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 LYS A 55 -3.08 74.57 REMARK 500 1 TRP A 56 -73.90 -106.10 REMARK 500 1 GLU A 59 -23.31 -147.50 REMARK 500 1 LYS A 61 -83.46 -121.05 REMARK 500 1 THR A 62 86.54 37.24 REMARK 500 2 ARG A 1 36.04 -176.55 REMARK 500 2 ARG A 5 50.12 38.78 REMARK 500 2 GLN A 6 -76.24 -65.11 REMARK 500 2 TRP A 56 -60.17 -126.02 REMARK 500 2 GLU A 59 -45.79 -155.52 REMARK 500 2 THR A 62 110.46 71.23 REMARK 500 3 ARG A 3 -176.35 -171.27 REMARK 500 3 THR A 7 -178.42 56.27 REMARK 500 3 PHE A 22 -80.07 -90.97 REMARK 500 3 ARG A 24 23.50 -74.18 REMARK 500 3 LYS A 55 -0.62 71.27 REMARK 500 3 LYS A 58 39.82 -144.97 REMARK 500 3 GLU A 59 -49.01 -152.84 REMARK 500 3 ASN A 60 36.57 -79.80 REMARK 500 3 LYS A 61 -76.83 57.02 REMARK 500 3 THR A 62 149.99 67.55 REMARK 500 4 ARG A 1 87.16 -60.19 REMARK 500 4 ARG A 3 126.17 76.07 REMARK 500 4 GLN A 6 -97.31 -59.17 REMARK 500 4 THR A 7 -165.67 46.51 REMARK 500 4 ARG A 29 -75.16 -55.57 REMARK 500 4 CYS A 39 51.90 75.18 REMARK 500 4 LYS A 55 -38.84 99.68 REMARK 500 4 GLU A 59 31.57 -159.21 REMARK 500 4 LYS A 61 -68.69 67.74 REMARK 500 4 THR A 62 148.76 64.05 REMARK 500 5 GLN A 6 -79.67 -91.33 REMARK 500 5 THR A 7 -12.53 86.01 REMARK 500 5 TYR A 8 -175.65 78.00 REMARK 500 5 PHE A 22 -80.56 -96.34 REMARK 500 5 LEU A 38 -82.80 -80.64 REMARK 500 5 CYS A 39 33.25 164.36 REMARK 500 5 LYS A 55 -14.63 88.07 REMARK 500 5 TRP A 56 -72.09 -105.06 REMARK 500 5 LYS A 57 7.58 -65.01 REMARK 500 5 GLU A 59 -11.49 -156.02 REMARK 500 5 LYS A 61 -68.69 65.07 REMARK 500 5 THR A 62 94.79 48.88 REMARK 500 6 LYS A 2 -177.23 60.31 REMARK 500 6 ARG A 3 78.49 70.57 REMARK 500 6 GLN A 6 -76.96 -75.61 REMARK 500 6 THR A 7 174.60 50.64 REMARK 500 6 LYS A 55 -13.10 103.60 REMARK 500 6 GLU A 59 -38.36 -161.40 REMARK 500 6 THR A 62 116.39 77.68 REMARK 500 REMARK 500 THIS ENTRY HAS 177 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 LYS A 58 GLU A 59 2 149.40 REMARK 500 LYS A 58 GLU A 59 6 148.79 REMARK 500 LYS A 58 GLU A 59 16 149.78 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 11 0.09 SIDE CHAIN REMARK 500 1 TYR A 25 0.08 SIDE CHAIN REMARK 500 1 PHE A 49 0.08 SIDE CHAIN REMARK 500 1 ARG A 52 0.15 SIDE CHAIN REMARK 500 2 TYR A 11 0.09 SIDE CHAIN REMARK 500 2 PHE A 20 0.12 SIDE CHAIN REMARK 500 2 ARG A 30 0.11 SIDE CHAIN REMARK 500 2 ARG A 31 0.09 SIDE CHAIN REMARK 500 2 ARG A 52 0.26 SIDE CHAIN REMARK 500 3 TYR A 8 0.09 SIDE CHAIN REMARK 500 3 ARG A 24 0.32 SIDE CHAIN REMARK 500 3 ARG A 31 0.10 SIDE CHAIN REMARK 500 3 PHE A 49 0.12 SIDE CHAIN REMARK 500 4 ARG A 3 0.08 SIDE CHAIN REMARK 500 4 TYR A 8 0.10 SIDE CHAIN REMARK 500 4 ARG A 10 0.10 SIDE CHAIN REMARK 500 4 PHE A 20 0.09 SIDE CHAIN REMARK 500 4 TYR A 25 0.10 SIDE CHAIN REMARK 500 4 ARG A 29 0.10 SIDE CHAIN REMARK 500 4 ARG A 31 0.10 SIDE CHAIN REMARK 500 4 ARG A 43 0.09 SIDE CHAIN REMARK 500 5 TYR A 8 0.06 SIDE CHAIN REMARK 500 5 TYR A 11 0.07 SIDE CHAIN REMARK 500 5 PHE A 20 0.14 SIDE CHAIN REMARK 500 5 ARG A 30 0.13 SIDE CHAIN REMARK 500 5 ARG A 52 0.18 SIDE CHAIN REMARK 500 6 ARG A 3 0.11 SIDE CHAIN REMARK 500 6 TYR A 8 0.11 SIDE CHAIN REMARK 500 6 PHE A 20 0.08 SIDE CHAIN REMARK 500 6 ARG A 30 0.16 SIDE CHAIN REMARK 500 6 ARG A 31 0.14 SIDE CHAIN REMARK 500 6 ARG A 52 0.24 SIDE CHAIN REMARK 500 7 TYR A 8 0.10 SIDE CHAIN REMARK 500 7 PHE A 20 0.08 SIDE CHAIN REMARK 500 7 ARG A 24 0.08 SIDE CHAIN REMARK 500 7 ARG A 31 0.09 SIDE CHAIN REMARK 500 7 ARG A 53 0.08 SIDE CHAIN REMARK 500 8 ARG A 24 0.18 SIDE CHAIN REMARK 500 8 ARG A 28 0.11 SIDE CHAIN REMARK 500 9 TYR A 8 0.09 SIDE CHAIN REMARK 500 9 TYR A 11 0.07 SIDE CHAIN REMARK 500 9 ARG A 24 0.08 SIDE CHAIN REMARK 500 9 ARG A 52 0.27 SIDE CHAIN REMARK 500 9 ARG A 53 0.17 SIDE CHAIN REMARK 500 10 ARG A 5 0.20 SIDE CHAIN REMARK 500 10 TYR A 8 0.09 SIDE CHAIN REMARK 500 10 ARG A 10 0.08 SIDE CHAIN REMARK 500 10 ARG A 29 0.13 SIDE CHAIN REMARK 500 10 ARG A 31 0.26 SIDE CHAIN REMARK 500 10 ARG A 43 0.08 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 103 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 18 GLU A 15 -12.91 REMARK 500 REMARK 500 REMARK: NULL DBREF 1HOM A 1 67 UNP P02833 ANTP_DROME 297 363 SEQRES 1 A 68 MET ARG LYS ARG GLY ARG GLN THR TYR THR ARG TYR GLN SEQRES 2 A 68 THR LEU GLU LEU GLU LYS GLU PHE HIS PHE ASN ARG TYR SEQRES 3 A 68 LEU THR ARG ARG ARG ARG ILE GLU ILE ALA HIS ALA LEU SEQRES 4 A 68 CYS LEU THR GLU ARG GLN ILE LYS ILE TRP PHE GLN ASN SEQRES 5 A 68 ARG ARG MET LYS TRP LYS LYS GLU ASN LYS THR LYS GLY SEQRES 6 A 68 GLU PRO GLY HELIX 1 1 THR A 9 ASN A 23 1 15 HELIX 2 2 THR A 27 LEU A 38 1 12 HELIX 3 3 THR A 41 MET A 54 1 14 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