HEADER HYDROLASE 14-FEB-17 5N5K TITLE HUMAN CATALYTIC MMP-12 IN COMPLEX WITH 5-(1,2-DITHIOLAN-3-YL)-N-(3- TITLE 2 HYDROXYPROPYL)PENTANAMIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: MACROPHAGE METALLOELASTASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: MME,MACROPHAGE ELASTASE,HME,MATRIX METALLOPROTEINASE-12,MMP- COMPND 5 12; COMPND 6 EC: 3.4.24.65; COMPND 7 ENGINEERED: YES; COMPND 8 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 MMP-12, LIPOIC ACID, INHIBITOR, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR V.CALDERONE REVDAT 3 17-JAN-24 5N5K 1 LINK REVDAT 2 22-NOV-17 5N5K 1 JRNL REVDAT 1 01-NOV-17 5N5K 0 JRNL AUTH M.FRAGAI,G.COMITO,L.DI CESARE MANNELLI,R.GUALDANI, JRNL AUTH 2 V.CALDERONE,A.LOUKA,B.RICHICHI,O.FRANCESCONI,A.ANGELI, JRNL AUTH 3 A.NOCENTINI,P.GRATTERI,P.CHIARUGI,C.GHELARDINI, JRNL AUTH 4 F.TADINI-BUONINSEGNI,C.T.SUPURAN,C.NATIVI JRNL TITL LIPOYL-HOMOTAURINE DERIVATIVE (ADM_12) REVERTS JRNL TITL 2 OXALIPLATIN-INDUCED NEUROPATHY AND REDUCES CANCER CELLS JRNL TITL 3 MALIGNANCY BY INHIBITING CARBONIC ANHYDRASE IX (CAIX). JRNL REF J. MED. CHEM. V. 60 9003 2017 JRNL REFN ISSN 1520-4804 JRNL PMID 29048889 JRNL DOI 10.1021/ACS.JMEDCHEM.7B01237 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0158 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.62 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.1 REMARK 3 NUMBER OF REFLECTIONS : 12282 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) : 0.170 REMARK 3 R VALUE (WORKING SET) : 0.167 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 647 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 510 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 61.30 REMARK 3 BIN R VALUE (WORKING SET) : 0.5780 REMARK 3 BIN FREE R VALUE SET COUNT : 27 REMARK 3 BIN FREE R VALUE : 0.6550 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1227 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 26 REMARK 3 SOLVENT ATOMS : 169 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.32 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.14000 REMARK 3 B22 (A**2) : -0.47000 REMARK 3 B33 (A**2) : -0.40000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.11000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.145 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.144 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.096 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.307 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.948 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.901 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1283 ; 0.024 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 1131 ; 0.005 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1735 ; 2.160 ; 1.925 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2614 ; 1.225 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 155 ; 7.036 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 63 ;32.953 ;23.175 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 188 ;13.199 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 7 ;14.032 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 178 ; 0.138 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1457 ; 0.012 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 294 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 624 ; 1.153 ; 1.047 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 622 ; 1.092 ; 1.042 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 777 ; 1.879 ; 1.561 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 778 ; 1.885 ; 1.564 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 659 ; 2.236 ; 1.293 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 659 ; 2.099 ; 1.293 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 959 ; 3.480 ; 1.843 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 1612 ; 7.686 ;14.791 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 1584 ; 7.467 ;14.386 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL 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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 108 A 901 REMARK 3 ORIGIN FOR THE GROUP (A): -14.8182 0.2582 10.2238 REMARK 3 T TENSOR REMARK 3 T11: 0.0271 T22: 0.0432 REMARK 3 T33: 0.0261 T12: 0.0009 REMARK 3 T13: -0.0254 T23: 0.0036 REMARK 3 L TENSOR REMARK 3 L11: 0.4015 L22: 0.2367 REMARK 3 L33: 0.3837 L12: -0.2619 REMARK 3 L13: -0.0204 L23: 0.1607 REMARK 3 S TENSOR REMARK 3 S11: -0.0359 S12: -0.0455 S13: 0.0121 REMARK 3 S21: 0.0434 S22: 0.0358 S23: -0.0211 REMARK 3 S31: 0.0203 S32: 0.0466 S33: 0.0001 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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 5N5K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-FEB-17. REMARK 100 THE DEPOSITION ID IS D_1200003215. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-JAN-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : SEALED TUBE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : OXFORD DIFFRACTION ENHANCE ULTRA REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : OXFORD ONYX CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12935 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 25.630 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.5 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : 0.06200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 24.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 78.3 REMARK 200 DATA REDUNDANCY IN SHELL : 4.20 REMARK 200 R MERGE FOR SHELL (I) : 0.42000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.650 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: 1Y93 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS-HCL, 20% PEG 6000, PH 8.0, REMARK 280 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 25.39500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.08500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 25.39500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 30.08500 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 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 530 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7690 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -59.0 KCAL/MOL 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 519 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 523 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 564 LIES ON A SPECIAL POSITION. 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 NH1 ARG A 135 O HOH A 401 1.56 REMARK 500 NH1 ARG A 110 O HOH A 402 1.72 REMARK 500 O HOH A 542 O HOH A 559 1.82 REMARK 500 O HOH A 517 O HOH A 566 2.13 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 NH2 ARG A 110 NH2 ARG A 165 3455 2.01 REMARK 500 O HOH A 490 O HOH A 543 2555 2.11 REMARK 500 NZ LYS A 177 OXT GLY A 263 3545 2.14 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 ARG A 165 NE - CZ - NH1 ANGL. DEV. = 5.2 DEGREES REMARK 500 ARG A 165 NE - CZ - NH2 ANGL. DEV. = -5.1 DEGREES REMARK 500 ASP A 171 CB - CG - OD1 ANGL. DEV. = 5.8 DEGREES REMARK 500 ARG A 256 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 HIS A 168 33.41 -140.05 REMARK 500 ASP A 170 -166.35 -120.45 REMARK 500 HIS A 206 -141.18 -134.58 REMARK 500 ILE A 245 0.81 -67.41 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 569 DISTANCE = 6.93 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 CA A 304 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 124 OD1 REMARK 620 2 ASP A 124 OD2 54.8 REMARK 620 3 GLU A 199 O 161.1 138.1 REMARK 620 4 GLU A 199 OE1 88.1 85.6 80.5 REMARK 620 5 GLU A 201 O 124.3 77.7 74.5 117.9 REMARK 620 6 HOH A 503 O 82.9 137.2 81.6 87.3 140.9 REMARK 620 7 HOH A 507 O 86.4 101.9 101.1 165.6 76.1 78.8 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 303 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 158 O REMARK 620 2 GLY A 190 O 171.1 REMARK 620 3 GLY A 192 O 91.5 95.5 REMARK 620 4 ASP A 194 OD1 85.8 99.6 90.8 REMARK 620 5 HOH A 414 O 90.0 82.6 174.8 94.2 REMARK 620 6 HOH A 434 O 85.8 90.0 79.9 167.3 95.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 302 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 168 NE2 REMARK 620 2 ASP A 170 OD2 106.5 REMARK 620 3 HIS A 183 NE2 124.8 113.5 REMARK 620 4 HIS A 196 ND1 108.4 94.4 104.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 305 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 175 OD1 REMARK 620 2 GLY A 176 O 86.9 REMARK 620 3 GLY A 178 O 89.1 88.6 REMARK 620 4 ILE A 180 O 88.2 175.1 90.6 REMARK 620 5 ASP A 198 OD2 93.5 89.2 176.5 91.8 REMARK 620 6 GLU A 201 OE1 179.4 93.6 91.2 91.3 86.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 218 NE2 REMARK 620 2 HIS A 222 NE2 94.9 REMARK 620 3 HIS A 228 NE2 101.1 96.8 REMARK 620 4 HAE A 306 O2 120.5 142.7 88.1 REMARK 620 5 HAE A 306 O 98.5 95.7 155.6 69.5 REMARK 620 N 1 2 3 4 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 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue HAE A 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 8NW A 307 DBREF 5N5K A 108 263 UNP P39900 MMP12_HUMAN 108 263 SEQADV 5N5K ASP A 171 UNP P39900 PHE 171 ENGINEERED MUTATION SEQRES 1 A 156 VAL TRP ARG LYS HIS TYR ILE THR TYR ARG ILE ASN ASN SEQRES 2 A 156 TYR THR PRO ASP MET ASN ARG GLU ASP VAL ASP TYR ALA SEQRES 3 A 156 ILE ARG LYS ALA PHE GLN VAL TRP SER ASN VAL THR PRO SEQRES 4 A 156 LEU LYS PHE SER LYS ILE ASN THR GLY MET ALA ASP ILE SEQRES 5 A 156 LEU VAL VAL PHE ALA ARG GLY ALA HIS GLY ASP ASP HIS SEQRES 6 A 156 ALA PHE ASP GLY LYS GLY GLY ILE LEU ALA HIS ALA PHE SEQRES 7 A 156 GLY PRO GLY SER GLY ILE GLY GLY ASP ALA HIS PHE ASP SEQRES 8 A 156 GLU ASP GLU PHE TRP THR THR HIS SER GLY GLY THR ASN SEQRES 9 A 156 LEU PHE LEU THR ALA VAL HIS GLU ILE GLY HIS SER LEU SEQRES 10 A 156 GLY LEU GLY HIS SER SER ASP PRO LYS ALA VAL MET PHE SEQRES 11 A 156 PRO THR TYR LYS TYR VAL ASP ILE ASN THR PHE ARG LEU SEQRES 12 A 156 SER ALA ASP ASP ILE ARG GLY ILE GLN SER LEU TYR GLY HET ZN A 301 1 HET ZN A 302 1 HET CA A 303 1 HET CA A 304 1 HET CA A 305 1 HET HAE A 306 5 HET 8NW A 307 16 HETNAM ZN ZINC ION HETNAM CA CALCIUM ION HETNAM HAE ACETOHYDROXAMIC ACID HETNAM 8NW 5-[(3~{S})-1,2-DITHIOLAN-3-YL]-~{N}-(3-OXIDANYLPROPYL) HETNAM 2 8NW PENTANAMIDE FORMUL 2 ZN 2(ZN 2+) FORMUL 4 CA 3(CA 2+) FORMUL 7 HAE C2 H5 N O2 FORMUL 8 8NW C11 H21 N O2 S2 FORMUL 9 HOH *169(H2 O) HELIX 1 AA1 ASN A 126 ASN A 143 1 18 HELIX 2 AA2 LEU A 212 LEU A 224 1 13 HELIX 3 AA3 SER A 251 GLY A 263 1 13 SHEET 1 AA1 5 LYS A 148 LYS A 151 0 SHEET 2 AA1 5 TYR A 113 ILE A 118 1 N ILE A 114 O LYS A 148 SHEET 3 AA1 5 ILE A 159 ALA A 164 1 O VAL A 161 N ARG A 117 SHEET 4 AA1 5 ALA A 195 ASP A 198 1 O PHE A 197 N VAL A 162 SHEET 5 AA1 5 ALA A 182 ALA A 184 -1 N HIS A 183 O HIS A 196 SHEET 1 AA2 2 TRP A 203 THR A 204 0 SHEET 2 AA2 2 THR A 210 ASN A 211 1 O THR A 210 N THR A 204 LINK OD1 ASP A 124 CA CA A 304 1555 1555 2.51 LINK OD2 ASP A 124 CA CA A 304 1555 1555 2.35 LINK O ASP A 158 CA CA A 303 1555 1555 2.17 LINK NE2 HIS A 168 ZN ZN A 302 1555 1555 2.02 LINK OD2 ASP A 170 ZN ZN A 302 1555 1555 1.97 LINK OD1 ASP A 175 CA CA A 305 1555 1555 2.37 LINK O GLY A 176 CA CA A 305 1555 1555 2.23 LINK O GLY A 178 CA CA A 305 1555 1555 2.27 LINK O ILE A 180 CA CA A 305 1555 1555 2.30 LINK NE2 HIS A 183 ZN ZN A 302 1555 1555 2.06 LINK O GLY A 190 CA CA A 303 1555 1555 2.34 LINK O GLY A 192 CA CA A 303 1555 1555 2.18 LINK OD1 ASP A 194 CA CA A 303 1555 1555 2.36 LINK ND1 HIS A 196 ZN ZN A 302 1555 1555 2.01 LINK OD2 ASP A 198 CA CA A 305 1555 1555 2.26 LINK O GLU A 199 CA CA A 304 1555 1555 2.35 LINK OE1 GLU A 199 CA CA A 304 1555 1555 2.38 LINK O GLU A 201 CA CA A 304 1555 1555 2.35 LINK OE1 GLU A 201 CA CA A 305 1555 1555 2.32 LINK NE2 HIS A 218 ZN ZN A 301 1555 1555 2.11 LINK NE2 HIS A 222 ZN ZN A 301 1555 1555 2.09 LINK NE2 HIS A 228 ZN ZN A 301 1555 1555 2.01 LINK ZN ZN A 301 O2 HAE A 306 1555 1555 2.07 LINK ZN ZN A 301 O HAE A 306 1555 1555 2.09 LINK CA CA A 303 O HOH A 414 1555 1555 2.31 LINK CA CA A 303 O HOH A 434 1555 1555 2.35 LINK CA CA A 304 O HOH A 503 1555 3545 2.33 LINK CA CA A 304 O HOH A 507 1555 1555 2.38 SITE 1 AC1 5 HIS A 218 HIS A 222 HIS A 228 HAE A 306 SITE 2 AC1 5 8NW A 307 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 414 HOH A 434 SITE 1 AC4 5 ASP A 124 GLU A 199 GLU A 201 HOH A 503 SITE 2 AC4 5 HOH A 507 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 10 ILE A 180 ALA A 182 HIS A 183 HIS A 218 SITE 2 AC6 10 GLU A 219 HIS A 222 HIS A 228 ZN A 301 SITE 3 AC6 10 8NW A 307 HOH A 515 SITE 1 AC7 17 GLY A 179 LEU A 181 LEU A 214 THR A 215 SITE 2 AC7 17 HIS A 218 GLU A 219 VAL A 235 PHE A 237 SITE 3 AC7 17 PRO A 238 THR A 239 TYR A 240 LYS A 241 SITE 4 AC7 17 ZN A 301 HAE A 306 HOH A 403 HOH A 488 SITE 5 AC7 17 HOH A 501 CRYST1 50.790 60.170 53.730 90.00 114.61 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 0.019689 0.000000 0.009018 0.00000 SCALE2 0.000000 0.016620 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020471 0.00000