HEADER IMMUNE SYSTEM 18-DEC-01 1KN4 TITLE CATALYTIC ANTIBODY D2.3 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: IG ANTIBODY D2.3 (LIGHT CHAIN); COMPND 3 CHAIN: L; COMPND 4 MOL_ID: 2; COMPND 5 MOLECULE: IG ANTIBODY D2.3 (HEAVY CHAIN); COMPND 6 CHAIN: H SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 7 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 8 ORGANISM_TAXID: 10090 KEYWDS ABZYME, TRANSITION STATE ANALOG, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR B.GIGANT,M.KNOSSOW REVDAT 5 30-OCT-24 1KN4 1 REMARK REVDAT 4 16-AUG-23 1KN4 1 REMARK LINK REVDAT 3 24-FEB-09 1KN4 1 VERSN REVDAT 2 01-APR-03 1KN4 1 JRNL REVDAT 1 13-MAR-02 1KN4 0 JRNL AUTH L.J.D'SOUZA,B.GIGANT,M.KNOSSOW,B.S.GREEN JRNL TITL REMARKABLE REMOTE CHIRAL RECOGNITION IN A REACTION MEDIATED JRNL TITL 2 BY A CATALYTIC ANTIBODY. JRNL REF J.AM.CHEM.SOC. V. 124 2114 2002 JRNL REFN ISSN 0002-7863 JRNL PMID 11878955 JRNL DOI 10.1021/JA0170504 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1811954.890 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 94.7 REMARK 3 NUMBER OF REFLECTIONS : 42809 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) : 0.213 REMARK 3 FREE R VALUE : 0.246 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2180 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.99 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 5196 REMARK 3 BIN R VALUE (WORKING SET) : 0.2750 REMARK 3 BIN FREE R VALUE : 0.2790 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.20 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 283 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.017 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3389 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 31 REMARK 3 SOLVENT ATOMS : 151 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.94000 REMARK 3 B22 (A**2) : 0.94000 REMARK 3 B33 (A**2) : -1.89000 REMARK 3 B12 (A**2) : 1.01000 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) : 0.23 REMARK 3 ESD FROM SIGMAA (A) : 0.22 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.27 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.20 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.011 REMARK 3 BOND ANGLES (DEGREES) : 1.800 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 28.70 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.690 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.870 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 3.020 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.990 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.330 ; 2.500 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1KN4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-DEC-01. REMARK 100 THE DEPOSITION ID IS D_1000015131. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-DEC-98 REMARK 200 TEMPERATURE (KELVIN) : 278.0 REMARK 200 PH : 7.00 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : LURE REMARK 200 BEAMLINE : DW32 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.963 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : BENT MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE 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 : 43212 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.5 REMARK 200 DATA REDUNDANCY : 2.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.04390 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.300 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: 1YEC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.91 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG600, ZNSO4, CACODYLATE, PH 7.00, REMARK 280 VAPOR DIFFUSION, HANGING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 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+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 52.93500 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 105.87000 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 105.87000 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 52.93500 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4 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: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5450 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19320 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -144.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: L, H 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: 11190 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 38530 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -348.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: L, H 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 158.80500 REMARK 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4420 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 45300 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -384.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 158.80500 REMARK 350 APPLY THE FOLLOWING TO CHAINS: H REMARK 350 BIOMT1 3 -0.500000 -0.866025 0.000000 39.12550 REMARK 350 BIOMT2 3 0.866025 -0.500000 0.000000 67.76735 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 52.93500 REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 39.12550 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 67.76735 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 105.87000 REMARK 350 REMARK 350 BIOMOLECULE: 4 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1910 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22860 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -162.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 APPLY THE FOLLOWING TO CHAINS: H REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 39.12550 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 67.76735 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 105.87000 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 LEU L 160 CA - CB - CG ANGL. DEV. = 13.8 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 VAL L 51 -44.13 71.47 REMARK 500 THR L 200 0.23 -69.82 REMARK 500 ASN L 212 -131.88 -140.57 REMARK 500 SER H 41 64.35 31.36 REMARK 500 ILE H 48 -63.60 -94.06 REMARK 500 THR H 82B 71.67 42.05 REMARK 500 VAL H 127 -39.76 -159.57 REMARK 500 THR H 132 -146.62 67.79 REMARK 500 SER H 134 -75.06 84.22 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 PDE IS PARA-NITROPHENYL PHOSPHONOBUTANOYL D-ALANINE REMARK 600 (NO2-C6H5-O-PO2-CH2-CH2-CH2-CO-NH-CH(CH3)-COOH) 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 L 553 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS L 49 NE2 REMARK 620 2 ASP H 100C OD1 106.0 REMARK 620 3 HOH H 251 O 96.6 97.5 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN L 556 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP L 60 OD2 REMARK 620 2 HOH L 560 O 130.6 REMARK 620 3 HOH L 606 O 125.3 85.0 REMARK 620 4 HOH L 624 O 84.3 126.2 108.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN L 554 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS L 93 ND1 REMARK 620 2 HOH L 561 O 117.7 REMARK 620 3 HOH L 573 O 93.3 105.2 REMARK 620 4 ASP H 181 OD1 110.0 114.9 113.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN L 555 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP L 151 OD1 REMARK 620 2 HIS L 189 ND1 110.8 REMARK 620 3 HOH L 604 O 82.0 105.0 REMARK 620 4 HOH L 605 O 116.6 120.9 114.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN L 557 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH L 605 O REMARK 620 2 HOH L 606 O 110.9 REMARK 620 3 HOH L 644 O 100.3 80.4 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN L 558 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH L 604 O REMARK 620 2 HOH L 615 O 82.0 REMARK 620 3 HOH L 624 O 123.5 85.3 REMARK 620 4 HOH L 638 O 67.2 148.7 106.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN L 559 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH L 573 O REMARK 620 2 HOH L 625 O 100.6 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN L 553 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN L 554 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN L 555 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN L 556 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN L 557 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN L 558 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN L 559 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PDE L 551 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1YEC RELATED DB: PDB REMARK 900 STRUCTURE OF A CATALYTIC ANTIBODY IGG2A FAB FRAGMENT (D2.3) REMARK 900 RELATED ID: 1YEF RELATED DB: PDB REMARK 900 STRUCTURE OF IGG2A FAB FRAGMENT (D2.3) COMPLEXED WITH SUBSTRATE REMARK 900 ANALOGUE REMARK 900 RELATED ID: 1YEG RELATED DB: PDB REMARK 900 STRUCTURE OF IGG2A FAB FRAGMENT (D2.3) COMPLEXED WITH REACTION REMARK 900 PRODUCT REMARK 900 RELATED ID: 1YEH RELATED DB: PDB REMARK 900 STRUCTURE OF IGG2A FAB FRAGMENT REMARK 900 RELATED ID: 1YEI RELATED DB: PDB REMARK 900 CATALYTIC ANTIBODY D2.3 COMPLEX REMARK 900 RELATED ID: 1YEJ RELATED DB: PDB REMARK 900 CATALYTIC ANTIBODY COMPLEX REMARK 900 RELATED ID: 1YEK RELATED DB: PDB REMARK 900 CATALYTIC ANTIBODY D2.3 COMPLEX REMARK 900 RELATED ID: 1KN2 RELATED DB: PDB REMARK 900 CATALYTIC ANTIBODY D2.3 COMPLEX REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE SEQUENCES OF THE CONSTANT DOMAINS OF THE HEAVY CHAINS. REMARK 999 (RESIDUES H106 - H223) AND OF THE LIGHT CHAINS REMARK 999 (RESIDUES L107 - L214) HAVE NOT BEEN DETERMINED FOR THIS REMARK 999 IMMUNOGLOBULIN. THEY HAVE BEEN ASSIGNED THE CONSENSUS REMARK 999 SEQUENCE FOR THE CONSTANT DOMAIN OF MOUSE KAPPA LIGHT REMARK 999 CHAIN AND FOR THE FIRST CONSTANT DOMAIN OF MOUSE GROUP REMARK 999 2A HEAVY CHAINS. DBREF 1KN4 L 1 214 UNP Q8K0F8 Q8K0F8_MOUSE 21 239 DBREF 1KN4 H 1 223 PDB 1KN4 1KN4 1 223 SEQRES 1 L 219 ASP ILE VAL MET THR GLN SER PRO LEU THR LEU SER VAL SEQRES 2 L 219 THR ILE GLY GLN PRO ALA SER ILE SER CYS LYS SER SER SEQRES 3 L 219 GLN SER LEU LEU TYR SER ASN GLY LYS THR TYR LEU ASN SEQRES 4 L 219 TRP LEU LEU GLN ARG PRO GLY GLN SER PRO LYS ARG LEU SEQRES 5 L 219 ILE HIS LEU VAL SER LYS LEU ASP SER GLY VAL PRO ASP SEQRES 6 L 219 ARG ILE THR GLY SER GLY SER GLY THR ASP PHE THR LEU SEQRES 7 L 219 LYS ILE SER ARG VAL GLU ALA ALA ASP LEU GLY VAL TYR SEQRES 8 L 219 TYR CYS VAL GLN GLY THR HIS PHE PRO TYR THR PHE GLY SEQRES 9 L 219 GLY GLY THR LYS LEU GLU ILE LEU ARG ALA ASP ALA ALA SEQRES 10 L 219 PRO THR VAL SER ILE PHE PRO PRO SER SER GLU GLN LEU SEQRES 11 L 219 THR SER GLY GLY ALA SER VAL VAL CYS PHE LEU ASN ASN SEQRES 12 L 219 PHE TYR PRO LYS ASP ILE ASN VAL LYS TRP LYS ILE ASP SEQRES 13 L 219 GLY SER GLU ARG GLN ASN GLY VAL LEU ASN SER TRP THR SEQRES 14 L 219 ASP GLN ASP SER LYS ASP SER THR TYR SER MET SER SER SEQRES 15 L 219 THR LEU THR LEU THR LYS ASP GLU TYR GLU ARG HIS ASN SEQRES 16 L 219 SER TYR THR CYS GLU ALA THR HIS LYS THR SER THR SER SEQRES 17 L 219 PRO ILE VAL LYS SER PHE ASN ARG ASN GLU CYS SEQRES 1 H 222 GLU MET GLN LEU GLN GLN SER GLY ALA GLU LEU LEU ARG SEQRES 2 H 222 PRO GLY THR SER VAL LYS LEU SER CYS LYS THR SER GLY SEQRES 3 H 222 TYR ILE PHE THR SER TYR TRP ILE HIS TRP VAL LYS GLN SEQRES 4 H 222 ARG SER GLY GLN GLY LEU GLU TRP ILE ALA ARG ILE TYR SEQRES 5 H 222 PRO GLY THR GLY SER THR TYR TYR ASN GLU LYS PHE LYS SEQRES 6 H 222 GLY LYS ALA THR LEU THR ALA ASP LYS SER SER SER THR SEQRES 7 H 222 ALA TYR MET GLN LEU SER THR LEU LYS SER GLU ASP SER SEQRES 8 H 222 ALA VAL TYR PHE CYS THR ARG TRP GLY PHE ILE PRO VAL SEQRES 9 H 222 ARG GLU ASP TYR VAL MET ASP TYR TRP GLY GLN GLY THR SEQRES 10 H 222 LEU VAL THR VAL SER SER ALA LYS THR THR ALA PRO SER SEQRES 11 H 222 VAL TYR PRO LEU ALA PRO VAL CYS GLY ASP THR THR GLY SEQRES 12 H 222 SER SER VAL THR LEU GLY CYS LEU VAL LYS GLY TYR PHE SEQRES 13 H 222 PRO GLU PRO VAL THR LEU THR TRP ASN SER GLY SER LEU SEQRES 14 H 222 SER SER GLY VAL HIS THR PHE PRO ALA VAL LEU GLN SER SEQRES 15 H 222 ASP LEU TYR THR LEU SER SER SER VAL THR VAL THR SER SEQRES 16 H 222 SER THR TRP PRO SER GLN SER ILE THR CYS ASN VAL ALA SEQRES 17 H 222 HIS PRO ALA SER SER THR LYS VAL ASP LYS LYS ILE GLU SEQRES 18 H 222 PRO HET ZN L 553 1 HET ZN L 554 1 HET ZN L 555 1 HET ZN L 556 1 HET ZN L 557 1 HET ZN L 558 1 HET ZN L 559 1 HET PDE L 551 24 HETNAM ZN ZINC ION HETNAM PDE PARA-NITROPHENYL PHOSPHONOBUTANOYL D-ALANINE FORMUL 3 ZN 7(ZN 2+) FORMUL 10 PDE C13 H17 N2 O8 P FORMUL 11 HOH *151(H2 O) HELIX 1 1 GLU L 79 LEU L 83 5 5 HELIX 2 2 SER L 121 SER L 127 1 7 HELIX 3 3 LYS L 183 GLU L 187 1 5 HELIX 4 4 ILE H 28 TYR H 32 5 5 HELIX 5 5 GLU H 61 LYS H 64 5 4 HELIX 6 6 LYS H 83 SER H 87 5 5 HELIX 7 7 SER H 161 SER H 163 5 3 HELIX 8 8 PRO H 211 SER H 214 5 4 SHEET 1 A 4 MET L 4 SER L 7 0 SHEET 2 A 4 ALA L 19 SER L 25 -1 O SER L 22 N SER L 7 SHEET 3 A 4 ASP L 70 ILE L 75 -1 O PHE L 71 N CYS L 23 SHEET 4 A 4 ILE L 62 SER L 67 -1 N THR L 63 O LYS L 74 SHEET 1 B 5 LYS L 53 LEU L 54 0 SHEET 2 B 5 LYS L 45 HIS L 49 -1 N HIS L 49 O LYS L 53 SHEET 3 B 5 LEU L 33 GLN L 38 -1 N TRP L 35 O LEU L 47 SHEET 4 B 5 GLY L 84 GLN L 90 -1 O TYR L 87 N LEU L 36 SHEET 5 B 5 THR L 97 PHE L 98 -1 O THR L 97 N GLN L 90 SHEET 1 C 6 LYS L 53 LEU L 54 0 SHEET 2 C 6 LYS L 45 HIS L 49 -1 N HIS L 49 O LYS L 53 SHEET 3 C 6 LEU L 33 GLN L 38 -1 N TRP L 35 O LEU L 47 SHEET 4 C 6 GLY L 84 GLN L 90 -1 O TYR L 87 N LEU L 36 SHEET 5 C 6 THR L 102 ILE L 106 -1 O LEU L 104 N GLY L 84 SHEET 6 C 6 THR L 10 VAL L 13 1 N LEU L 11 O GLU L 105 SHEET 1 D 4 THR L 114 PHE L 118 0 SHEET 2 D 4 GLY L 129 PHE L 139 -1 O ASN L 137 N THR L 114 SHEET 3 D 4 TYR L 173 THR L 182 -1 O TYR L 173 N PHE L 139 SHEET 4 D 4 VAL L 159 TRP L 163 -1 N SER L 162 O SER L 176 SHEET 1 E 4 SER L 153 ARG L 155 0 SHEET 2 E 4 ASN L 145 ILE L 150 -1 N TRP L 148 O ARG L 155 SHEET 3 E 4 SER L 191 THR L 197 -1 O GLU L 195 N LYS L 147 SHEET 4 E 4 ILE L 205 ASN L 210 -1 O LYS L 207 N CYS L 194 SHEET 1 F 4 GLN H 3 GLN H 6 0 SHEET 2 F 4 VAL H 18 SER H 25 -1 O LYS H 23 N GLN H 5 SHEET 3 F 4 THR H 77 LEU H 82 -1 O MET H 80 N LEU H 20 SHEET 4 F 4 ALA H 67 ASP H 72 -1 N ASP H 72 O THR H 77 SHEET 1 G 5 THR H 57 TYR H 59 0 SHEET 2 G 5 LEU H 45 ILE H 51 -1 N ARG H 50 O TYR H 58 SHEET 3 G 5 ILE H 34 GLN H 39 -1 N LYS H 38 O GLU H 46 SHEET 4 G 5 ALA H 88 ARG H 94 -1 O PHE H 91 N VAL H 37 SHEET 5 G 5 TYR H 102 TRP H 103 -1 O TYR H 102 N ARG H 94 SHEET 1 H 6 THR H 57 TYR H 59 0 SHEET 2 H 6 LEU H 45 ILE H 51 -1 N ARG H 50 O TYR H 58 SHEET 3 H 6 ILE H 34 GLN H 39 -1 N LYS H 38 O GLU H 46 SHEET 4 H 6 ALA H 88 ARG H 94 -1 O PHE H 91 N VAL H 37 SHEET 5 H 6 THR H 107 VAL H 111 -1 O VAL H 109 N ALA H 88 SHEET 6 H 6 GLU H 10 LEU H 12 1 N LEU H 12 O THR H 110 SHEET 1 I 4 SER H 120 LEU H 124 0 SHEET 2 I 4 SER H 135 TYR H 145 -1 O LEU H 141 N TYR H 122 SHEET 3 I 4 LEU H 182 THR H 192 -1 O LEU H 185 N VAL H 142 SHEET 4 I 4 VAL H 169 THR H 171 -1 N HIS H 170 O SER H 188 SHEET 1 J 4 SER H 120 LEU H 124 0 SHEET 2 J 4 SER H 135 TYR H 145 -1 O LEU H 141 N TYR H 122 SHEET 3 J 4 LEU H 182 THR H 192 -1 O LEU H 185 N VAL H 142 SHEET 4 J 4 VAL H 175 GLN H 177 -1 N GLN H 177 O LEU H 182 SHEET 1 K 3 THR H 151 TRP H 155 0 SHEET 2 K 3 THR H 204 HIS H 210 -1 O ASN H 207 N THR H 154 SHEET 3 K 3 THR H 215 LYS H 220 -1 O LYS H 219 N CYS H 206 SSBOND 1 CYS L 23 CYS L 88 1555 1555 2.03 SSBOND 2 CYS L 134 CYS L 194 1555 1555 2.02 SSBOND 3 CYS H 22 CYS H 92 1555 1555 2.02 SSBOND 4 CYS H 140 CYS H 206 1555 1555 2.02 LINK NE2 HIS L 49 ZN ZN L 553 1555 1555 2.25 LINK OD2 ASP L 60 ZN ZN L 556 4456 1555 2.01 LINK ND1 HIS L 93 ZN ZN L 554 1555 1555 2.25 LINK OD1 ASP L 151 ZN ZN L 555 1555 1555 2.11 LINK ND1 HIS L 189 ZN ZN L 555 1555 1555 2.36 LINK ZN ZN L 553 OD1 ASP H 100C 1555 1555 2.05 LINK ZN ZN L 553 O HOH H 251 1555 1555 1.54 LINK ZN ZN L 554 O HOH L 561 1555 1555 1.62 LINK ZN ZN L 554 O HOH L 573 1555 1555 1.65 LINK ZN ZN L 554 OD1 ASP H 181 1555 5665 1.83 LINK ZN ZN L 555 O HOH L 604 1555 1555 1.60 LINK ZN ZN L 555 O HOH L 605 1555 1555 1.82 LINK ZN ZN L 556 O HOH L 560 1555 1555 2.15 LINK ZN ZN L 556 O HOH L 606 1555 1555 1.79 LINK ZN ZN L 556 O HOH L 624 1555 1555 1.82 LINK ZN ZN L 557 O HOH L 605 1555 1555 1.67 LINK ZN ZN L 557 O HOH L 606 1555 1555 1.70 LINK ZN ZN L 557 O HOH L 644 1555 1555 2.25 LINK ZN ZN L 558 O HOH L 604 1555 1555 2.04 LINK ZN ZN L 558 O HOH L 615 1555 1555 1.93 LINK ZN ZN L 558 O HOH L 624 1555 1555 1.74 LINK ZN ZN L 558 O HOH L 638 1555 1455 2.67 LINK ZN ZN L 559 O HOH L 573 1555 1555 2.07 LINK ZN ZN L 559 O HOH L 625 1555 1555 1.74 CISPEP 1 SER L 7 PRO L 8 0 -0.25 CISPEP 2 PHE L 94 PRO L 95 0 0.15 CISPEP 3 TYR L 140 PRO L 141 0 -1.60 CISPEP 4 PHE H 146 PRO H 147 0 -0.31 CISPEP 5 GLU H 148 PRO H 149 0 0.34 CISPEP 6 TRP H 197 PRO H 198 0 0.02 SITE 1 AC1 4 ASP H 100C HOH H 251 HIS L 49 LYS L 53 SITE 1 AC2 5 ASP H 181 HIS L 93 ZN L 559 HOH L 561 SITE 2 AC2 5 HOH L 573 SITE 1 AC3 6 ASP L 151 HIS L 189 ZN L 557 ZN L 558 SITE 2 AC3 6 HOH L 604 HOH L 605 SITE 1 AC4 6 ASP L 60 ZN L 557 ZN L 558 HOH L 560 SITE 2 AC4 6 HOH L 606 HOH L 624 SITE 1 AC5 5 ZN L 555 ZN L 556 HOH L 605 HOH L 606 SITE 2 AC5 5 HOH L 644 SITE 1 AC6 6 ZN L 555 ZN L 556 HOH L 604 HOH L 615 SITE 2 AC6 6 HOH L 624 HOH L 638 SITE 1 AC7 4 SER H 112 ZN L 554 HOH L 573 HOH L 625 SITE 1 AC8 13 HIS H 35 VAL H 37 ARG H 50 TRP H 95 SITE 2 AC8 13 PHE H 97 TYR H 100D ASN L 34 VAL L 89 SITE 3 AC8 13 GLY L 91 PHE L 94 TYR L 96 PHE L 98 SITE 4 AC8 13 HOH L 562 CRYST1 78.251 78.251 158.805 90.00 90.00 120.00 P 31 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 0.012779 0.007378 0.000000 0.00000 SCALE2 0.000000 0.014756 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006297 0.00000