1Y93 - Header Asymmetric Unit

HEADER HYDROLASE 14-DEC-04 1Y93

TITLE CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN MMP12 COMPLEXED TITLE 2 WITH ACETOHYDROXAMIC ACID AT ATOMIC RESOLUTION

COMPND MOL_ID: 1; COMPND 2 MOLECULE: MACROPHAGE METALLOELASTASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC DOMAIN; COMPND 5 SYNONYM: HME, MATRIX METALLOPROTEINASE-12, MMP-12, MACROPHAGE COMPND 6 ELASTASE, ME; COMPND 7 EC: 3.4.24.65; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES

SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: MMP12, HME; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562

KEYWDS MATRIX METALLOPROTEINASE, MMP12, ELASTASE, COMPLEX (ELASTASE- KEYWDS 2 INHIBITOR), METALLO ELASTASE, ACETOHYDROXAMIC ACID, HYDROLASE

EXPDTA X-RAY DIFFRACTION

AUTHOR I.BERTINI,V.CALDERONE,M.COSENZA,M.FRAGAI,Y.-M.LEE,C.LUCHINAT, AUTHOR 2 S.MANGANI,B.TERNI,P.TURANO

REVDAT 4 13-JUL-11 1Y93 1 VERSN REVDAT 3 16-MAR-10 1Y93 1 ATOM REVDAT 2 24-FEB-09 1Y93 1 VERSN REVDAT 1 26-APR-05 1Y93 0

JRNL AUTH I.BERTINI,V.CALDERONE,M.COSENZA,M.FRAGAI,Y.-M.LEE, JRNL AUTH 2 C.LUCHINAT,S.MANGANI,B.TERNI,P.TURANO JRNL TITL CONFORMATIONAL VARIABILITY OF MATRIX METALLOPROTEINASES: JRNL TITL 2 BEYOND A SINGLE 3D STRUCTURE JRNL REF PROC.NATL.ACAD.SCI.USA V. 102 5334 2005 JRNL REFN ISSN 0027-8424 JRNL PMID 15809432 JRNL DOI 10.1073/PNAS.0407106102

REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH I.BERTINI,V.CALDERONE,M.FRAGAI,C.LUCHINAT,S.MANGANI,B.TERNI REMARK 1 TITL X-RAY STRUCTURES OF BINARY AND TERNARY REMARK 1 TITL 2 ENZYME-PRODUCT-INHIBITOR COMPLEXES OF MATRIX REMARK 1 TITL 3 METALLOPROTEINASES REMARK 1 REF ANGEW.CHEM.INT.ED.ENGL. V. 42 2673 2003 REMARK 1 REFN ISSN 1433-7851 REMARK 1 PMID 12813751 REMARK 1 DOI 10.1002/ANIE.200350957 REMARK 1 REFERENCE 2 REMARK 1 AUTH R.LANG,A.KOCOUREK,M.BRAUN,H.TSCHESCHE,R.HUBER,W.BODE, REMARK 1 AUTH 2 K.MASKOS REMARK 1 TITL SUBSTRATE SPECIFICITY DETERMINANTS OF HUMAN MACROPHAGE REMARK 1 TITL 2 ELASTASE (MMP-12) BASED ON THE 1.1 A CRYSTAL STRUCTURE REMARK 1 REF J.MOL.BIOL. V. 312 731 2001 REMARK 1 REFN ISSN 0022-2836

REMARK 2 REMARK 2 RESOLUTION. 1.03 ANGSTROMS.

REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0003 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.03 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 13.99 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 65283 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 + TEST SET) : 0.157 REMARK 3 R VALUE (WORKING SET) : 0.156 REMARK 3 FREE R VALUE : 0.168 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.800 REMARK 3 FREE R VALUE TEST SET COUNT : 5517 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.03 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.06 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4551 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.00 REMARK 3 BIN R VALUE (WORKING SET) : 0.3030 REMARK 3 BIN FREE R VALUE SET COUNT : 382 REMARK 3 BIN FREE R VALUE : 0.3230 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1238 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 10 REMARK 3 SOLVENT ATOMS : 287 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 6.63 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 8.69 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.04000 REMARK 3 B22 (A**2) : 0.09000 REMARK 3 B33 (A**2) : -0.23000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.12000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.028 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.027 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.016 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.642 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.957 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1279 ; 0.011 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 1100 ; 0.004 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1734 ; 1.379 ; 1.904 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2545 ; 0.721 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 157 ; 6.382 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 63 ;34.082 ;23.175 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 188 ;11.832 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 7 ;14.416 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 178 ; 0.075 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1469 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 292 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 347 ; 0.216 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1284 ; 0.185 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 672 ; 0.200 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 760 ; 0.090 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 219 ; 0.129 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 23 ; 0.110 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 23 ; 0.183 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 59 ; 0.199 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 47 ; 0.146 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 787 ; 1.125 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 331 ; 0.523 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1242 ; 1.635 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 555 ; 2.210 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 492 ; 3.254 ; 4.500 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 2695 ; 1.104 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 293 ; 3.907 ; 3.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 2343 ; 2.650 ; 3.000 REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS

REMARK 4 REMARK 4 1Y93 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11

REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-JAN-05. REMARK 100 THE RCSB ID CODE IS RCSB031270.

REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-JUL-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ELETTRA REMARK 200 BEAMLINE : 5.2R REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.99993 REMARK 200 MONOCHROMATOR : DOUBLE-CRYSTAL, SI(111) AND REMARK 200 SI(220) REMARK 200 OPTICS : DOUBLE-CRYSTAL, SI(111) AND REMARK 200 SI(220) REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 70833 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.020 REMARK 200 RESOLUTION RANGE LOW (A) : 48.400 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.05700 REMARK 200 R SYM (I) : 0.05700 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 5.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.02 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.08 REMARK 200 COMPLETENESS FOR SHELL (%) : 84.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.25100 REMARK 200 R SYM FOR SHELL (I) : 0.25100 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1RMZ REMARK 200 REMARK 200 REMARK: NULL

REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: TRIS, PEG 6000, ACETOHYDROXAMIC ACID, REMARK 280 PH 8.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K

REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 25.45650 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.77600 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 25.45650 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 29.77600 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL

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 300 REMARK: THE PROTEIN IS MONOMERIC IN VIVO AND THERE IS ONE MOLECULE REMARK 300 IN THE ASYMMETRIC UNIT.

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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 396 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 330 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 377 LIES ON A SPECIAL POSITION.

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 105

REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 HE2 HIS A 168 ZN ZN A 265 1.11 REMARK 500 HE2 HIS A 183 ZN ZN A 265 1.14 REMARK 500 HD1 HIS A 196 ZN ZN A 265 1.16 REMARK 500 HE2 HIS A 218 ZN ZN A 264 1.17 REMARK 500 HE2 HIS A 228 ZN ZN A 264 1.18 REMARK 500 H ASN A 211 HH TYR A 240 1.19 REMARK 500 HE2 HIS A 222 ZN ZN A 264 1.20 REMARK 500 HD2 HIS A 206 H GLY A 208 1.41 REMARK 500 REMARK 500 REMARK: NULL 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 HE3 MET A 156 HG1 THR A 247 3455 1.44 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 ASP A 170 CB - CG - OD2 ANGL. DEV. = 5.6 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 HIS A 168 33.03 -140.46 REMARK 500 HIS A 206 -153.93 -135.07 REMARK 500 REMARK 500 REMARK: NULL

REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 530 DISTANCE = 5.09 ANGSTROMS REMARK 525 HOH A 536 DISTANCE = 5.02 ANGSTROMS REMARK 525 HOH A 566 DISTANCE = 5.03 ANGSTROMS

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 A 264 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HAE A 301 O2 REMARK 620 2 HAE A 301 O 73.6 REMARK 620 3 HIS A 228 NE2 89.6 156.1 REMARK 620 4 HOH A 408 O 84.6 79.1 82.5 REMARK 620 5 HIS A 218 NE2 161.4 90.5 102.2 82.9 REMARK 620 6 HIS A 222 NE2 96.7 102.3 96.4 178.3 96.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 265 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 168 NE2 REMARK 620 2 ASP A 170 OD1 108.3 REMARK 620 3 HIS A 183 NE2 118.5 113.4 REMARK 620 4 HIS A 196 ND1 107.3 96.0 111.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 266 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 194 OD2 REMARK 620 2 GLY A 190 O 100.6 REMARK 620 3 HOH A 346 O 96.0 84.2 REMARK 620 4 ASP A 158 O 89.1 169.8 91.8 REMARK 620 5 GLY A 192 O 90.4 92.4 173.2 90.6 REMARK 620 6 HOH A 308 O 167.9 87.7 93.7 83.2 80.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 267 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 199 O REMARK 620 2 GLU A 199 OE2 81.7 REMARK 620 3 HOH A 319 O 81.2 87.5 REMARK 620 4 ASP A 124 OD1 160.9 85.2 84.4 REMARK 620 5 GLU A 201 O 76.4 118.2 142.3 122.3 REMARK 620 6 ASP A 124 OD2 139.0 85.2 137.0 52.7 76.1 REMARK 620 7 HOH A 310 O 100.3 165.2 78.4 89.0 76.4 102.1 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 268 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 176 O REMARK 620 2 GLY A 178 O 85.5 REMARK 620 3 ILE A 180 O 176.5 92.4 REMARK 620 4 ASP A 198 OD1 88.4 173.9 93.6 REMARK 620 5 GLU A 201 OE2 93.0 90.5 89.8 90.7 REMARK 620 6 ASP A 175 OD2 88.1 84.4 89.0 94.5 174.7 REMARK 620 N 1 2 3 4 5

REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 264 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 265 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 266 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 267 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 268 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HAE A 301

REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1OS2 RELATED DB: PDB REMARK 900 TERNARY ENZYME-PRODUCT-INHIBITOR COMPLEXES OF HUMAN MMP12 REMARK 900 RELATED ID: 1OS9 RELATED DB: PDB REMARK 900 BINARY ENZYME-PRODUCT-INHIBITOR COMPLEXES OF HUMAN MMP12 REMARK 900 RELATED ID: 1JK3 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN MMP-12 (MACROPHAGE ELASTASE) AT REMARK 900 TRUE ATOMIC RESOLUTION REMARK 900 RELATED ID: 1RMZ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN MMP12 REMARK 900 COMPLEXED WITH THE INHIBITOR NNGH AT 1.3 A RESOLUTION

DBREF 1Y93 A 106 263 UNP P39900 MMP12_HUMAN 106 263

SEQADV 1Y93 MET A 105 UNP P39900 INITIATING METHIONINE SEQADV 1Y93 ASP A 171 UNP P39900 PHE 171 ENGINEERED

SEQRES 1 A 159 MET GLY PRO VAL TRP ARG LYS HIS TYR ILE THR TYR ARG SEQRES 2 A 159 ILE ASN ASN TYR THR PRO ASP MET ASN ARG GLU ASP VAL SEQRES 3 A 159 ASP TYR ALA ILE ARG LYS ALA PHE GLN VAL TRP SER ASN SEQRES 4 A 159 VAL THR PRO LEU LYS PHE SER LYS ILE ASN THR GLY MET SEQRES 5 A 159 ALA ASP ILE LEU VAL VAL PHE ALA ARG GLY ALA HIS GLY SEQRES 6 A 159 ASP ASP HIS ALA PHE ASP GLY LYS GLY GLY ILE LEU ALA SEQRES 7 A 159 HIS ALA PHE GLY PRO GLY SER GLY ILE GLY GLY ASP ALA SEQRES 8 A 159 HIS PHE ASP GLU ASP GLU PHE TRP THR THR HIS SER GLY SEQRES 9 A 159 GLY THR ASN LEU PHE LEU THR ALA VAL HIS GLU ILE GLY SEQRES 10 A 159 HIS SER LEU GLY LEU GLY HIS SER SER ASP PRO LYS ALA SEQRES 11 A 159 VAL MET PHE PRO THR TYR LYS TYR VAL ASP ILE ASN THR SEQRES 12 A 159 PHE ARG LEU SER ALA ASP ASP ILE ARG GLY ILE GLN SER SEQRES 13 A 159 LEU TYR GLY

HET ZN A 264 1 HET ZN A 265 1 HET CA A 266 1 HET CA A 267 1 HET CA A 268 1 HET HAE A 301 9

HETNAM ZN ZINC ION HETNAM CA CALCIUM ION HETNAM HAE ACETOHYDROXAMIC ACID

FORMUL 2 ZN 2(ZN 2+) FORMUL 4 CA 3(CA 2+) FORMUL 7 HAE C2 H5 N O2 FORMUL 8 HOH *287(H2 O)

HELIX 1 1 ASN A 126 ASN A 143 1 18 HELIX 2 2 LEU A 212 LEU A 224 1 13 HELIX 3 3 ASP A 244 PHE A 248 5 5 HELIX 4 4 SER A 251 SER A 260 1 10

SHEET 1 A 5 LYS A 148 LYS A 151 0 SHEET 2 A 5 TYR A 113 ILE A 118 1 N ILE A 114 O LYS A 148 SHEET 3 A 5 ILE A 159 ALA A 164 1 O VAL A 161 N ARG A 117 SHEET 4 A 5 ALA A 195 ASP A 198 1 O PHE A 197 N VAL A 162 SHEET 5 A 5 ALA A 182 ALA A 184 -1 N HIS A 183 O HIS A 196 SHEET 1 B 2 TRP A 203 THR A 204 0 SHEET 2 B 2 THR A 210 ASN A 211 1 O THR A 210 N THR A 204

LINK ZN ZN A 264 O2 HAE A 301 1555 1555 2.13 LINK ZN ZN A 264 O HAE A 301 1555 1555 2.07 LINK ZN ZN A 264 NE2 HIS A 228 1555 1555 2.03 LINK ZN ZN A 264 O HOH A 408 1555 1555 2.65 LINK ZN ZN A 264 NE2 HIS A 218 1555 1555 2.03 LINK ZN ZN A 264 NE2 HIS A 222 1555 1555 2.07 LINK ZN ZN A 265 NE2 HIS A 168 1555 1555 1.98 LINK ZN ZN A 265 OD1 ASP A 170 1555 1555 1.91 LINK ZN ZN A 265 NE2 HIS A 183 1555 1555 1.99 LINK ZN ZN A 265 ND1 HIS A 196 1555 1555 2.02 LINK CA CA A 266 OD2 ASP A 194 1555 1555 2.42 LINK CA CA A 266 O GLY A 190 1555 1555 2.28 LINK CA CA A 266 O HOH A 346 1555 1555 2.33 LINK CA CA A 266 O ASP A 158 1555 1555 2.33 LINK CA CA A 266 O GLY A 192 1555 1555 2.24 LINK CA CA A 266 O HOH A 308 1555 1555 2.37 LINK CA CA A 267 O GLU A 199 1555 1555 2.31 LINK CA CA A 267 OE2 GLU A 199 1555 1555 2.35 LINK CA CA A 267 O HOH A 319 1555 1555 2.40 LINK CA CA A 267 OD1 ASP A 124 1555 1555 2.52 LINK CA CA A 267 O GLU A 201 1555 1555 2.39 LINK CA CA A 267 OD2 ASP A 124 1555 1555 2.36 LINK CA CA A 267 O HOH A 310 1555 1555 2.37 LINK CA CA A 268 O GLY A 176 1555 1555 2.26 LINK CA CA A 268 O GLY A 178 1555 1555 2.41 LINK CA CA A 268 O ILE A 180 1555 1555 2.25 LINK CA CA A 268 OD1 ASP A 198 1555 1555 2.34 LINK CA CA A 268 OE2 GLU A 201 1555 1555 2.17 LINK CA CA A 268 OD2 ASP A 175 1555 1555 2.25

SITE 1 AC1 5 HIS A 218 HIS A 222 HIS A 228 HAE A 301 SITE 2 AC1 5 HOH A 408 SITE 1 AC2 4 HIS A 168 ASP A 170 HIS A 183 HIS A 196 SITE 1 AC3 6 ASP A 158 GLY A 190 GLY A 192 ASP A 194 SITE 2 AC3 6 HOH A 308 HOH A 346 SITE 1 AC4 5 ASP A 124 GLU A 199 GLU A 201 HOH A 310 SITE 2 AC4 5 HOH A 319 SITE 1 AC5 6 ASP A 175 GLY A 176 GLY A 178 ILE A 180 SITE 2 AC5 6 ASP A 198 GLU A 201 SITE 1 AC6 9 ALA A 182 HIS A 218 GLU A 219 HIS A 222 SITE 2 AC6 9 HIS A 228 ZN A 264 HOH A 328 HOH A 408 SITE 3 AC6 9 HOH A 450

CRYST1 50.913 59.552 53.497 90.00 115.14 90.00 C 1 2 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 0.019641 0.000000 0.009217 0.00000

SCALE2 0.000000 0.016792 0.000000 0.00000

SCALE3 0.000000 0.000000 0.020649 0.00000