HEADER IMMUNE SYSTEM 14-MAR-05 2BMK TITLE FAB FRAGMENT OF PLP-DEPENDENT CATALYTIC ANTIBODY 15A9 IN COMPLEX WITH TITLE 2 PHOSPHOPYRIDOXYL-D-ALANINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: FAB FRAGMENT OF CATALYTIC ANTIBODY 15A9, LIGHT CHAIN; COMPND 3 CHAIN: A, L; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: FAB FRAGMENT OF CATALYTIC ANTIBODY 15A9, HEAVY CHAIN; COMPND 7 CHAIN: B, H; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 EXPRESSION_SYSTEM: MUS MUSCULUS; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 10090; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BALB/C; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: 15A9 MURINE HYBRIDOMA; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 11 ORGANISM_COMMON: MOUSE; SOURCE 12 ORGANISM_TAXID: 10090; SOURCE 13 EXPRESSION_SYSTEM: MUS MUSCULUS; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 10090; SOURCE 15 EXPRESSION_SYSTEM_STRAIN: BALB/C; SOURCE 16 EXPRESSION_SYSTEM_CELL_LINE: 15A9 MURINE HYBRIDOMA KEYWDS CATALYTIC ANTIBODY, TRANSAMINATION, PYRIDOXAL-PHOSPHATE, HAPTEN, KEYWDS 2 PHOSPHOPYRIDOXYL-L-LYSINE, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR B.GOLINELLI-PIMPANEAU,P.CHRISTEN REVDAT 5 27-FEB-19 2BMK 1 JRNL REMARK REVDAT 4 24-FEB-09 2BMK 1 VERSN REVDAT 3 16-AUG-06 2BMK 1 JRNL REVDAT 2 28-JUN-06 2BMK 1 JRNL REVDAT 1 03-MAR-06 2BMK 0 JRNL AUTH B.GOLINELLI-PIMPANEAU,C.LUTHI,P.CHRISTEN JRNL TITL STRUCTURAL BASIS FOR D-AMINO ACID TRANSAMINATION BY THE JRNL TITL 2 PYRIDOXAL 5'-PHOSPHATE-DEPENDENT CATALYTIC ANTIBODY 15A9. JRNL REF J. BIOL. CHEM. V. 281 23969 2006 JRNL REFN ISSN 0021-9258 JRNL PMID 16790434 JRNL DOI 10.1074/JBC.M602184200 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.I.GRAMATIKOVA,P.CHRISTEN REMARK 1 TITL MONOCLONAL ANTIBODIES AGAINST REMARK 1 TITL 2 N-ALPHA-(5'-PHOSPHOPYRIDOXYL)-L-LYSINE. REMARK 1 REF J.BIOL.CHEM. V. 272 9779 1997 REMARK 1 REFN ISSN 0021-9258 REMARK 1 PMID 9092511 REMARK 1 DOI 10.1074/JBC.272.15.9779 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 10000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 90.2 REMARK 3 NUMBER OF REFLECTIONS : 32247 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.210 REMARK 3 FREE R VALUE : 0.273 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3220 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 : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.40 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 275 REMARK 3 BIN R VALUE (WORKING SET) : 0.3152 REMARK 3 BIN FREE R VALUE : 0.3826 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 107 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 : 6565 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 48 REMARK 3 SOLVENT ATOMS : 354 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 44.06 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.02900 REMARK 3 B22 (A**2) : -3.53100 REMARK 3 B33 (A**2) : 3.50300 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.33700 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) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.379 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) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : 0.33 REMARK 3 BSOL : 37.74 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : PPD.PAR REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : PPD.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2BMK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-MAR-05. REMARK 100 THE DEPOSITION ID IS D_1290023330. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-JUL-03 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.00 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.931 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32263 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.34 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.59000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1WCB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 32.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30%PEG 3350, 200MM SODIUM IODIDE, 50MM REMARK 280 SODIUM ACETATE, PH6, VAPOR DIFFUSION, TEMPERATURE 298K, PH 6.00 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z 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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 40.57600 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: H, L 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 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 ALA B 129 REMARK 465 ALA B 130 REMARK 465 ALA H 129 REMARK 465 ALA H 130 REMARK 465 GLN H 131 REMARK 465 THR H 132 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 SER A 56 OG REMARK 470 ARG A 77 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 147 CG CD CE NZ REMARK 470 GLN A 156 CG CD OE1 NE2 REMARK 470 LYS A 169 CG CD CE NZ REMARK 470 ARG A 188 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 207 CG CD CE NZ REMARK 470 LYS B 43 CG CD CE NZ REMARK 470 LYS B 64 CG CD CE NZ REMARK 470 ARG B 83 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 115 CG CD CE NZ REMARK 470 GLN B 131 CG CD OE1 NE2 REMARK 470 THR B 132 OG1 CG2 REMARK 470 ASN B 133 CG OD1 ND2 REMARK 470 SER B 158 OG REMARK 470 GLN B 171 CG CD OE1 NE2 REMARK 470 ASP B 173 CG OD1 OD2 REMARK 470 GLU B 191 CG CD OE1 OE2 REMARK 470 LYS B 205 CG CD CE NZ REMARK 470 ARG B 213 CG CD NE CZ NH1 NH2 REMARK 470 ASP B 214 CA C O CB CG OD1 OD2 REMARK 470 ASN H 133 CG OD1 ND2 REMARK 470 SER H 158 OG REMARK 470 GLN H 171 CG CD OE1 NE2 REMARK 470 ASP H 173 CG OD1 OD2 REMARK 470 GLU H 191 CG CD OE1 OE2 REMARK 470 LYS H 205 CG CD CE NZ REMARK 470 LYS H 209 CG CD CE NZ REMARK 470 ASP H 214 CA C O CB CG OD1 OD2 REMARK 470 SER L 56 OG REMARK 470 ARG L 77 CG CD NE CZ NH1 NH2 REMARK 470 ASP L 184 CG OD1 OD2 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 THR A 51 -47.78 74.20 REMARK 500 PRO A 59 154.57 -48.39 REMARK 500 ALA A 84 -176.82 175.59 REMARK 500 TYR A 140 138.79 -170.05 REMARK 500 ASP A 143 102.02 -56.56 REMARK 500 PRO B 41 118.18 -35.46 REMARK 500 SER B 74 -75.14 -62.37 REMARK 500 ALA B 88 -177.16 179.89 REMARK 500 ASP B 95 -146.85 -89.39 REMARK 500 SER B 98 22.12 -75.53 REMARK 500 TYR B 99 -158.98 -130.56 REMARK 500 ASN B 133 -164.15 -125.44 REMARK 500 PRO B 147 -162.22 -102.11 REMARK 500 SER B 156 27.39 46.62 REMARK 500 SER B 190 -37.00 -137.50 REMARK 500 THR B 192 116.34 109.58 REMARK 500 LYS B 205 116.10 -161.21 REMARK 500 ALA H 88 -179.89 -176.12 REMARK 500 ASP H 95 -148.60 -92.32 REMARK 500 TYR H 99 -154.11 -119.27 REMARK 500 ASN H 100A 67.52 -100.51 REMARK 500 SER H 190 -36.28 -135.01 REMARK 500 THR H 192 128.67 92.83 REMARK 500 THR L 51 -49.99 74.05 REMARK 500 ALA L 84 -171.87 -179.27 REMARK 500 ASP L 143 110.20 -31.35 REMARK 500 GLN L 156 -69.85 -90.08 REMARK 500 REMARK 500 REMARK: NULL REMARK 700 REMARK 700 SHEET REMARK 700 THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN REMARK 700 ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, REMARK 700 TWO SHEETS ARE DEFINED. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IOD B1215 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IOD B1216 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IOD B1218 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IOD H1215 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IOD H1216 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IOD H1217 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PDD B1217 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PDD L1215 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1WC7 RELATED DB: PDB REMARK 900 FAB FRAGMENT OF PLP-DEPENDENT CATALYTIC ANTIBODY 15A9 IN COMPLEX REMARK 900 WITH PHOSPHOPYRIDOXYL -L-ALANINE REMARK 900 RELATED ID: 1WCB RELATED DB: PDB REMARK 900 PLP-DEPENDENT CATALYTIC ANTIBODY 15A9 IN COMPLEX WITH ITS HAPTEN DBREF 2BMK A 1 27 PDB 2BMK 2BMK 1 27 DBREF 2BMK A 29 214 PDB 2BMK 2BMK 29 214 DBREF 2BMK B 1 214 PDB 2BMK 2BMK 1 214 DBREF 2BMK H 1 214 PDB 2BMK 2BMK 1 214 DBREF 2BMK L 1 27 PDB 2BMK 2BMK 1 27 DBREF 2BMK L 29 214 PDB 2BMK 2BMK 29 214 SEQRES 1 A 213 ASP ILE GLU LEU THR GLN SER PRO ALA ILE MET ALA ALA SEQRES 2 A 213 SER PRO GLY GLU LYS VAL THR ILE THR CYS SER ALA THR SEQRES 3 A 213 SER GLY VAL ASN TYR MET HIS TRP PHE GLN GLN LYS PRO SEQRES 4 A 213 GLY THR SER PRO LYS LEU TRP ILE TYR SER THR SER ASN SEQRES 5 A 213 LEU ALA SER ALA VAL PRO ALA ARG PHE SER GLY SER GLY SEQRES 6 A 213 SER GLY THR SER TYR SER LEU THR ILE SER ARG MET GLU SEQRES 7 A 213 ALA GLU ASP ALA ALA THR TYR TYR CYS GLN GLN ARG SER SEQRES 8 A 213 THR TYR PRO PHE THR PHE GLY GLY GLY THR LYS LEU GLU SEQRES 9 A 213 LEU LYS ARG ALA ASP ALA ALA PRO THR VAL SER ILE PHE SEQRES 10 A 213 PRO PRO SER SER GLU GLN LEU THR SER GLY GLY ALA SER SEQRES 11 A 213 VAL VAL CYS PHE LEU ASN ASN PHE TYR PRO LYS ASP ILE SEQRES 12 A 213 ASN VAL LYS TRP LYS ILE ASP GLY SER GLU ARG GLN ASN SEQRES 13 A 213 GLY VAL LEU ASN SER TRP THR ASP GLN ASP SER LYS ASP SEQRES 14 A 213 SER THR TYR SER MET SER SER THR LEU THR LEU THR LYS SEQRES 15 A 213 ASP GLU TYR GLU ARG HIS ASN SER TYR THR CYS GLU ALA SEQRES 16 A 213 THR HIS LYS THR SER THR SER PRO ILE VAL LYS SER PHE SEQRES 17 A 213 ASN ARG ASN GLU CYS SEQRES 1 B 226 GLU VAL LYS LEU GLN GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 B 226 PRO GLY HIS SER LEU ARG LEU SER CYS ALA THR SER GLY SEQRES 3 B 226 PHE THR PHE THR ASP TYR TYR MET SER TRP VAL ARG GLN SEQRES 4 B 226 PRO PRO GLY LYS ALA LEU GLU TRP LEU GLY LEU ILE ARG SEQRES 5 B 226 ASN LYS ALA ASN GLY TYR THR LYS GLU TYR SER ALA SER SEQRES 6 B 226 VAL LYS GLY ARG PHE THR ILE SER ARG ASP ASN SER GLN SEQRES 7 B 226 SER ILE LEU TYR LEU GLN MET ASN ALA LEU ARG ALA GLU SEQRES 8 B 226 ASP SER ALA THR TYR TYR CYS VAL ARG ASP LYS GLY SER SEQRES 9 B 226 TYR GLY ASN TYR GLU ALA TRP PHE ALA TYR TRP GLY GLN SEQRES 10 B 226 GLY THR THR VAL THR VAL SER SER ALA LYS THR THR PRO SEQRES 11 B 226 PRO SER VAL TYR PRO LEU ALA PRO GLY SER ALA ALA GLN SEQRES 12 B 226 THR ASN SER MET VAL THR LEU GLY CYS LEU VAL LYS GLY SEQRES 13 B 226 TYR PHE PRO GLU PRO VAL THR VAL THR TRP ASN SER GLY SEQRES 14 B 226 SER LEU SER SER GLY VAL HIS THR PHE PRO ALA VAL LEU SEQRES 15 B 226 GLN SER ASP LEU TYR THR LEU SER SER SER VAL THR VAL SEQRES 16 B 226 PRO SER SER PRO ARG PRO SER GLU THR VAL THR CYS ASN SEQRES 17 B 226 VAL ALA HIS PRO ALA SER SER THR LYS VAL ASP LYS LYS SEQRES 18 B 226 ILE VAL PRO ARG ASP SEQRES 1 H 226 GLU VAL LYS LEU GLN GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 H 226 PRO GLY HIS SER LEU ARG LEU SER CYS ALA THR SER GLY SEQRES 3 H 226 PHE THR PHE THR ASP TYR TYR MET SER TRP VAL ARG GLN SEQRES 4 H 226 PRO PRO GLY LYS ALA LEU GLU TRP LEU GLY LEU ILE ARG SEQRES 5 H 226 ASN LYS ALA ASN GLY TYR THR LYS GLU TYR SER ALA SER SEQRES 6 H 226 VAL LYS GLY ARG PHE THR ILE SER ARG ASP ASN SER GLN SEQRES 7 H 226 SER ILE LEU TYR LEU GLN MET ASN ALA LEU ARG ALA GLU SEQRES 8 H 226 ASP SER ALA THR TYR TYR CYS VAL ARG ASP LYS GLY SER SEQRES 9 H 226 TYR GLY ASN TYR GLU ALA TRP PHE ALA TYR TRP GLY GLN SEQRES 10 H 226 GLY THR THR VAL THR VAL SER SER ALA LYS THR THR PRO SEQRES 11 H 226 PRO SER VAL TYR PRO LEU ALA PRO GLY SER ALA ALA GLN SEQRES 12 H 226 THR ASN SER MET VAL THR LEU GLY CYS LEU VAL LYS GLY SEQRES 13 H 226 TYR PHE PRO GLU PRO VAL THR VAL THR TRP ASN SER GLY SEQRES 14 H 226 SER LEU SER SER GLY VAL HIS THR PHE PRO ALA VAL LEU SEQRES 15 H 226 GLN SER ASP LEU TYR THR LEU SER SER SER VAL THR VAL SEQRES 16 H 226 PRO SER SER PRO ARG PRO SER GLU THR VAL THR CYS ASN SEQRES 17 H 226 VAL ALA HIS PRO ALA SER SER THR LYS VAL ASP LYS LYS SEQRES 18 H 226 ILE VAL PRO ARG ASP SEQRES 1 L 213 ASP ILE GLU LEU THR GLN SER PRO ALA ILE MET ALA ALA SEQRES 2 L 213 SER PRO GLY GLU LYS VAL THR ILE THR CYS SER ALA THR SEQRES 3 L 213 SER GLY VAL ASN TYR MET HIS TRP PHE GLN GLN LYS PRO SEQRES 4 L 213 GLY THR SER PRO LYS LEU TRP ILE TYR SER THR SER ASN SEQRES 5 L 213 LEU ALA SER ALA VAL PRO ALA ARG PHE SER GLY SER GLY SEQRES 6 L 213 SER GLY THR SER TYR SER LEU THR ILE SER ARG MET GLU SEQRES 7 L 213 ALA GLU ASP ALA ALA THR TYR TYR CYS GLN GLN ARG SER SEQRES 8 L 213 THR TYR PRO PHE THR PHE GLY GLY GLY THR LYS LEU GLU SEQRES 9 L 213 LEU LYS ARG ALA ASP ALA ALA PRO THR VAL SER ILE PHE SEQRES 10 L 213 PRO PRO SER SER GLU GLN LEU THR SER GLY GLY ALA SER SEQRES 11 L 213 VAL VAL CYS PHE LEU ASN ASN PHE TYR PRO LYS ASP ILE SEQRES 12 L 213 ASN VAL LYS TRP LYS ILE ASP GLY SER GLU ARG GLN ASN SEQRES 13 L 213 GLY VAL LEU ASN SER TRP THR ASP GLN ASP SER LYS ASP SEQRES 14 L 213 SER THR TYR SER MET SER SER THR LEU THR LEU THR LYS SEQRES 15 L 213 ASP GLU TYR GLU ARG HIS ASN SER TYR THR CYS GLU ALA SEQRES 16 L 213 THR HIS LYS THR SER THR SER PRO ILE VAL LYS SER PHE SEQRES 17 L 213 ASN ARG ASN GLU CYS HET IOD B1215 1 HET IOD B1216 1 HET PDD B1217 21 HET IOD B1218 1 HET IOD H1215 1 HET IOD H1216 1 HET IOD H1217 1 HET PDD L1215 21 HETNAM IOD IODIDE ION HETNAM PDD N-(5'-PHOSPHOPYRIDOXYL)-D-ALANINE FORMUL 5 IOD 6(I 1-) FORMUL 7 PDD 2(C11 H17 N2 O7 P) FORMUL 13 HOH *354(H2 O) HELIX 1 1 GLU A 79 ALA A 83 5 5 HELIX 2 2 SER A 121 SER A 127 1 7 HELIX 3 3 LYS A 183 GLU A 187 1 5 HELIX 4 4 THR B 28 THR B 30 5 3 HELIX 5 5 ASN B 52A GLY B 54 5 5 HELIX 6 6 ARG B 83 SER B 87 5 5 HELIX 7 7 ASN B 100A TRP B 100E 5 5 HELIX 8 8 SER B 156 SER B 158 5 3 HELIX 9 9 PRO B 200 SER B 203 5 4 HELIX 10 10 THR H 28 TYR H 32 5 5 HELIX 11 11 ALA H 61 LYS H 64 5 4 HELIX 12 12 ARG H 83 SER H 87 5 5 HELIX 13 13 ASN H 100A TRP H 100E 5 5 HELIX 14 14 SER H 156 SER H 158 5 3 HELIX 15 15 PRO H 200 SER H 203 5 4 HELIX 16 16 GLU L 79 ALA L 83 5 5 HELIX 17 17 SER L 121 GLY L 128 1 8 HELIX 18 18 LYS L 183 GLU L 187 1 5 SHEET 1 AA 4 LEU A 4 SER A 7 0 SHEET 2 AA 4 VAL A 19 ALA A 25 -1 O THR A 22 N SER A 7 SHEET 3 AA 4 SER A 70 ILE A 75 -1 O TYR A 71 N CYS A 23 SHEET 4 AA 4 PHE A 62 SER A 67 -1 O SER A 63 N THR A 74 SHEET 1 AB 6 ILE A 10 ALA A 13 0 SHEET 2 AB 6 THR A 102 LEU A 106 1 O LYS A 103 N MET A 11 SHEET 3 AB 6 ALA A 84 GLN A 90 -1 O ALA A 84 N LEU A 104 SHEET 4 AB 6 HIS A 34 GLN A 38 -1 O HIS A 34 N GLN A 89 SHEET 5 AB 6 LYS A 45 TYR A 49 -1 O LYS A 45 N GLN A 37 SHEET 6 AB 6 ASN A 53 LEU A 54 -1 O ASN A 53 N TYR A 49 SHEET 1 AC 4 ILE A 10 ALA A 13 0 SHEET 2 AC 4 THR A 102 LEU A 106 1 O LYS A 103 N MET A 11 SHEET 3 AC 4 ALA A 84 GLN A 90 -1 O ALA A 84 N LEU A 104 SHEET 4 AC 4 THR A 97 PHE A 98 -1 O THR A 97 N GLN A 90 SHEET 1 AD 4 THR A 114 PHE A 118 0 SHEET 2 AD 4 GLY A 129 PHE A 139 -1 O VAL A 133 N PHE A 118 SHEET 3 AD 4 TYR A 173 THR A 182 -1 O TYR A 173 N PHE A 139 SHEET 4 AD 4 VAL A 159 TRP A 163 -1 O LEU A 160 N THR A 178 SHEET 1 AE 4 SER A 153 ARG A 155 0 SHEET 2 AE 4 ILE A 144 ILE A 150 -1 O TRP A 148 N ARG A 155 SHEET 3 AE 4 SER A 191 HIS A 198 -1 O THR A 193 N LYS A 149 SHEET 4 AE 4 ILE A 205 ASN A 210 -1 O ILE A 205 N ALA A 196 SHEET 1 BA 4 LYS B 3 SER B 7 0 SHEET 2 BA 4 LEU B 18 SER B 25 -1 O SER B 21 N SER B 7 SHEET 3 BA 4 ILE B 77 MET B 82 -1 O LEU B 78 N CYS B 22 SHEET 4 BA 4 PHE B 67 ASP B 72 -1 O THR B 68 N GLN B 81 SHEET 1 BB 6 LEU B 11 VAL B 12 0 SHEET 2 BB 6 THR B 107 VAL B 111 1 O THR B 110 N VAL B 12 SHEET 3 BB 6 ALA B 88 GLY B 97 -1 O ALA B 88 N VAL B 109 SHEET 4 BB 6 TYR B 32 GLN B 39 -1 O TYR B 33 N ASP B 95 SHEET 5 BB 6 GLU B 46 ILE B 51 -1 O GLU B 46 N ARG B 38 SHEET 6 BB 6 LYS B 57 TYR B 59 -1 O GLU B 58 N LEU B 50 SHEET 1 BC 4 LEU B 11 VAL B 12 0 SHEET 2 BC 4 THR B 107 VAL B 111 1 O THR B 110 N VAL B 12 SHEET 3 BC 4 ALA B 88 GLY B 97 -1 O ALA B 88 N VAL B 109 SHEET 4 BC 4 TYR B 102 TRP B 103 -1 O TYR B 102 N ARG B 94 SHEET 1 BD 4 SER B 120 LEU B 124 0 SHEET 2 BD 4 MET B 135 TYR B 145 -1 O GLY B 139 N LEU B 124 SHEET 3 BD 4 LEU B 174 PRO B 184 -1 O TYR B 175 N TYR B 145 SHEET 4 BD 4 VAL B 163 THR B 165 -1 O HIS B 164 N SER B 180 SHEET 1 BE 4 SER B 120 LEU B 124 0 SHEET 2 BE 4 MET B 135 TYR B 145 -1 O GLY B 139 N LEU B 124 SHEET 3 BE 4 LEU B 174 PRO B 184 -1 O TYR B 175 N TYR B 145 SHEET 4 BE 4 VAL B 169 GLN B 171 -1 O VAL B 169 N THR B 176 SHEET 1 BF 3 THR B 151 TRP B 154 0 SHEET 2 BF 3 THR B 194 HIS B 199 -1 O ASN B 196 N THR B 153 SHEET 3 BF 3 THR B 204 LYS B 209 -1 O THR B 204 N HIS B 199 SHEET 1 HA 4 LYS H 3 SER H 7 0 SHEET 2 HA 4 LEU H 18 SER H 25 -1 O SER H 21 N SER H 7 SHEET 3 HA 4 ILE H 77 MET H 82 -1 O LEU H 78 N CYS H 22 SHEET 4 HA 4 PHE H 67 ASP H 72 -1 O THR H 68 N GLN H 81 SHEET 1 HB 9 GLY H 10 VAL H 12 0 SHEET 2 HB 9 THR H 107 VAL H 111 1 O THR H 108 N GLY H 10 SHEET 3 HB 9 ALA H 88 ARG H 94 -1 O ALA H 88 N VAL H 109 SHEET 4 HB 9 LYS H 57 TYR H 59 0 SHEET 5 HB 9 GLU H 46 ILE H 51 -1 O LEU H 50 N GLU H 58 SHEET 6 HB 9 MET H 34 GLN H 39 -1 O MET H 34 N ILE H 51 SHEET 7 HB 9 ALA H 88 ARG H 94 -1 O THR H 89 N GLN H 39 SHEET 8 HB 9 TYR H 102 TRP H 103 -1 O TYR H 102 N ARG H 94 SHEET 9 HB 9 ALA H 88 ARG H 94 -1 N ARG H 94 O TYR H 102 SHEET 1 HC 7 SER H 120 LEU H 124 0 SHEET 2 HC 7 MET H 135 TYR H 145 -1 O GLY H 139 N LEU H 124 SHEET 3 HC 7 LEU H 174 PRO H 184 -1 O TYR H 175 N TYR H 145 SHEET 4 HC 7 VAL H 163 THR H 165 -1 O HIS H 164 N SER H 180 SHEET 5 HC 7 LEU H 174 PRO H 184 -1 O SER H 180 N HIS H 164 SHEET 6 HC 7 VAL H 169 GLN H 171 -1 O VAL H 169 N THR H 176 SHEET 7 HC 7 LEU H 174 PRO H 184 -1 O LEU H 174 N GLN H 171 SHEET 1 HD 3 THR H 151 TRP H 154 0 SHEET 2 HD 3 THR H 194 HIS H 199 -1 O ASN H 196 N THR H 153 SHEET 3 HD 3 THR H 204 LYS H 209 -1 O THR H 204 N HIS H 199 SHEET 1 LA 3 LEU L 4 SER L 7 0 SHEET 2 LA 3 VAL L 19 VAL L 30 -1 O THR L 22 N SER L 7 SHEET 3 LA 3 PHE L 62 ILE L 75 -1 O GLY L 68 N VAL L 30 SHEET 1 LB 9 ILE L 10 ALA L 13 0 SHEET 2 LB 9 THR L 102 LEU L 106 1 O LYS L 103 N MET L 11 SHEET 3 LB 9 ALA L 84 GLN L 90 -1 O ALA L 84 N LEU L 104 SHEET 4 LB 9 ASN L 53 LEU L 54 0 SHEET 5 LB 9 LYS L 45 TYR L 49 -1 O TYR L 49 N ASN L 53 SHEET 6 LB 9 HIS L 34 GLN L 38 -1 O TRP L 35 N TRP L 47 SHEET 7 LB 9 ALA L 84 GLN L 90 -1 O THR L 85 N GLN L 38 SHEET 8 LB 9 THR L 97 PHE L 98 -1 O THR L 97 N GLN L 90 SHEET 9 LB 9 ALA L 84 GLN L 90 -1 O GLN L 90 N THR L 97 SHEET 1 LC 4 THR L 114 PHE L 118 0 SHEET 2 LC 4 GLY L 129 PHE L 139 -1 O VAL L 133 N PHE L 118 SHEET 3 LC 4 TYR L 173 THR L 182 -1 O TYR L 173 N PHE L 139 SHEET 4 LC 4 VAL L 159 TRP L 163 -1 O LEU L 160 N THR L 178 SHEET 1 LD 4 SER L 153 GLU L 154 0 SHEET 2 LD 4 ASN L 145 ILE L 150 -1 O ILE L 150 N SER L 153 SHEET 3 LD 4 SER L 191 THR L 197 -1 O THR L 193 N LYS L 149 SHEET 4 LD 4 ILE L 205 ASN L 210 -1 O ILE L 205 N ALA L 196 SSBOND 1 CYS A 23 CYS A 88 1555 1555 2.05 SSBOND 2 CYS A 134 CYS A 194 1555 1555 2.04 SSBOND 3 CYS B 22 CYS B 92 1555 1555 2.04 SSBOND 4 CYS B 140 CYS B 195 1555 1555 2.03 SSBOND 5 CYS H 22 CYS H 92 1555 1555 2.04 SSBOND 6 CYS H 140 CYS H 195 1555 1555 2.03 SSBOND 7 CYS L 23 CYS L 88 1555 1555 2.05 SSBOND 8 CYS L 134 CYS L 194 1555 1555 2.03 CISPEP 1 SER A 7 PRO A 8 0 -0.15 CISPEP 2 TYR A 94 PRO A 95 0 -0.01 CISPEP 3 TYR A 140 PRO A 141 0 0.31 CISPEP 4 PHE B 146 PRO B 147 0 -0.04 CISPEP 5 GLU B 148 PRO B 149 0 0.10 CISPEP 6 ARG B 188 PRO B 189 0 -0.11 CISPEP 7 PHE H 146 PRO H 147 0 -0.37 CISPEP 8 GLU H 148 PRO H 149 0 0.16 CISPEP 9 ARG H 188 PRO H 189 0 0.09 CISPEP 10 SER L 7 PRO L 8 0 -0.20 CISPEP 11 TYR L 94 PRO L 95 0 -0.20 CISPEP 12 TYR L 140 PRO L 141 0 0.32 SITE 1 AC1 4 TYR B 32 GLY B 97 TYR B 99 TRP B 100E SITE 1 AC2 2 ASN B 52A ASN B 53 SITE 1 AC3 1 THR B 68 SITE 1 AC4 2 THR H 68 ASN H 82A SITE 1 AC5 4 GLY H 97 TYR H 99 ASN H 100A TRP H 100E SITE 1 AC6 2 GLY H 26 PHE H 27 SITE 1 AC7 12 TYR A 32 HIS A 34 ARG A 91 SER A 92 SITE 2 AC7 12 TYR A 94 TYR B 33 ARG B 52 ASP B 95 SITE 3 AC7 12 LYS B 96 HOH B2080 HOH B2081 HOH B2082 SITE 1 AC8 10 TYR H 33 ARG H 52 ASP H 95 TYR L 32 SITE 2 AC8 10 HIS L 34 ARG L 91 SER L 92 TYR L 94 SITE 3 AC8 10 HOH L2096 HOH L2097 CRYST1 63.152 81.152 79.331 90.00 90.35 90.00 P 1 21 1 4 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 0.015835 0.000000 0.000097 0.00000 SCALE2 0.000000 0.012323 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012606 0.00000 MTRIX1 1 0.999300 0.029100 0.024300 -8.86920 1 MTRIX2 1 0.029600 -0.999400 -0.020200 118.20190 1 MTRIX3 1 0.023700 0.020900 -0.999500 116.89560 1 MTRIX1 2 0.999300 0.036800 0.011300 -8.25040 1 MTRIX2 2 0.037000 -0.999200 -0.017700 117.51480 1 MTRIX3 2 0.010700 0.018100 -0.999800 117.52310 1 MASTER 368 0 8 18 90 0 12 12 0 0 0 70 END