HEADER HYDROLASE 29-DEC-16 5UE5 TITLE PROMMP-7 WITH HEPARIN OCTASACCHARIDE BOUND TO THE CATALYTIC DOMAIN CAVEAT 5UE5 IDS B 4 HAS WRONG CHIRALITY AT ATOM C1 SGN B 7 HAS WRONG CAVEAT 2 5UE5 CHIRALITY AT ATOM C1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: MATRILYSIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: MATRIN,MATRIX METALLOPROTEINASE-7,MMP-7,PUMP-1 PROTEASE, COMPND 5 UTERINE METALLOPROTEINASE; COMPND 6 EC: 3.4.24.23; 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: MMP7, MPSL1, PUMP1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS GLYCAN COMPLEX WITH PROTEIN, ENZYME COMPLEX WITH HEPARIN KEYWDS 2 OLIGOSACCHARIDE, ZYMOGEN, ALLOSTERIC EFFECTOR SITE, HYDROLASE EXPDTA SOLUTION NMR NUMMDL 16 AUTHOR Y.G.FULCHER,S.H.PRIOR,R.J.LINHARDT,S.R.VAN DOREN REVDAT 5 01-MAY-24 5UE5 1 HETSYN LINK REVDAT 4 29-JUL-20 5UE5 1 CAVEAT COMPND REMARK HETNAM REVDAT 4 2 1 LINK SITE ATOM REVDAT 3 01-JAN-20 5UE5 1 REMARK REVDAT 2 27-SEP-17 5UE5 1 REMARK REVDAT 1 19-JUL-17 5UE5 0 JRNL AUTH Y.G.FULCHER,S.H.PRIOR,S.MASUKO,L.LI,D.PU,F.ZHANG, JRNL AUTH 2 R.J.LINHARDT,S.R.VAN DOREN JRNL TITL GLYCAN ACTIVATION OF A SHEDDASE: ELECTROSTATIC RECOGNITION JRNL TITL 2 BETWEEN HEPARIN AND PROMMP-7. JRNL REF STRUCTURE V. 25 1100 2017 JRNL REFN ISSN 1878-4186 JRNL PMID 28648610 JRNL DOI 10.1016/J.STR.2017.05.019 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.H.PRIOR,Y.G.FULCHER,R.K.KOPPISETTI,A.JURKEVICH, REMARK 1 AUTH 2 S.R.VAN DOREN REMARK 1 TITL CHARGE-TRIGGERED MEMBRANE INSERTION OF MATRIX REMARK 1 TITL 2 METALLOPROTEINASE-7, SUPPORTER OF INNATE IMMUNITY AND REMARK 1 TITL 3 TUMORS. REMARK 1 REF STRUCTURE V. 23 2099 2015 REMARK 1 REFN ISSN 1878-4186 REMARK 1 PMID 26439767 REMARK 1 DOI 10.1016/J.STR.2015.08.013 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SYBYL X 2.1.1 REMARK 3 AUTHORS : TRIPOS / CERTARA REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 15000 STEPS OF REFINEMENT. EXPLICIT DISTANCE RESTRAINTS TO THE REMARK 3 TEMPO SPIN-LABELED REDUCING END OF HEPARIN DP8 WERE OBTAINED FROM REMARK 3 THE PRES (T2) USING AN EQUATION FROM BATTISTE AND WAGNER (2000, REMARK 3 BIOCHEMISTRY) SIMPLIFIED BY WHTC GREATER THAN1 TO THE FORM R EQUAL REMARK 3 TO 4KTC/T2 GIVEN BY KOPPISETTI ET AL. (2014, NATURE COMMS.). THE REMARK 3 ROTATIONAL CORRELATION TIME TC OF THE PROTEIN-HEPARIN COMPLEXES REMARK 3 WAS OBTAINED FROM AMIDE 15N CROSS-CORRELATION RATES NXY (LIU AND REMARK 3 PRESTEGARD, 2008, J. MAGN. RESON.) INTERPRETED BY THE SPECTRAL REMARK 3 DENSITY EXPRESSION USED IN THE TRACT APPROACH (LEE ET AL., 2006. REMARK 3 J. MAGN. RESON.). UPPER BOUNDS WERE SET AT 15% ABOVE THE DISTANCE REMARK 3 ESTIMATE. AN INTERMOLECULAR NOE FROM AN ARGININE BACKBONE AMIDE REMARK 3 FROM 2H/15N-LABELED ENZYME TO THE ANOMERIC PROTON H1 OF GLCNS6S 5 REMARK 3 OR 7 HAD AN UPPER BOUND OF 6 A. LOWER BOUNDS WERE IMPLICITLY AT REMARK 3 VAN DER WAALS DISTANCE. REMARK 3 AMBIGUOUS DISTANCE RESTRAINTS FROM ANY RESIDUE OF HEPARIN DP8 TO REMARK 3 EXPLICIT PROTEIN AMIDE GROUPS WERE APPLIED ON THE BASIS OF AMIDE REMARK 3 CHEMICAL SHIFT PERTURBATIONS FROM HEPARIN DP8 OR PROTECTION OF REMARK 3 AMIDES BY HEPARIN DP4 FROM LINE BROADENING BY GD.EDTA WITH DELTAT2 REMARK 3 GREATER THAN 37/SEC. AMBIGUOUS DISTANCE RESTRAINTS FROM ANY REMARK 3 RESIDUE OF HEPARIN DP8 TO LYSINE AMINO OR ARGININE UREIDO GROUPS REMARK 3 WERE ALSO APPLIED ON THE BASIS OF MUTATIONS THAT IMPAIRED REMARK 3 ACTIVATION OF PROMMP-7 BY HEPARIN DP16. THE COMBINATION OF THE REMARK 3 INTERMOLECULAR DISTANCE RESTRAINTS FROM THE EXPLICIT PRE AND NOE REMARK 3 MEASUREMENTS AND THE AMBIGUOUS SOURCES WERE USED TO DOCK REMARK 3 COORDINATES OF HEPARIN DP8 WITH THE NMR SOLUTION STRUCTURE OF REMARK 3 HUMAN PROMMP-7 OF PRIOR ET AL. (2015, STRUCTURE). TO ENABLE REMARK 3 MOLECULAR FLEXIBILITY WIDELY THROUGH THE PROMMP-7 AND HEPARIN DP8 REMARK 3 CHAINS WHILE MAINTAINING THE STRUCTURAL INTEGRITY OF THE PROMMP-7 REMARK 3 DURING THE RESTRAINED DOCKING SIMULATIONS, CYANA 2.1 (GUNTERT AND REMARK 3 BUCHNER, 2015, J. BIOMOL. NMR) WAS UTILIZED IN CONCERT WITH THE REMARK 3 INTRAMOLECULAR PROMMP-7 NOE-DERIVED DISTANCE RESTRAINTS AND REMARK 3 CHEMICAL SHIFT-DERIVED DIHEDRAL RESTRAINTS OF THE NMR STRUCTURE REMARK 3 (PRIOR ET AL., 2015, STRUCTURE). CYANA TOPOLOGY FILES DESCRIBING REMARK 3 THE SUGAR MONOMERS WERE DERIVED FROM TOPOLOGY FILES CURATED BY THE REMARK 3 AUTOMATED TOPOLOGY BUILDER (MALDE ET AL., 2011, J. CHEM. THEORY REMARK 3 COMPUT.) AND BASED ON ACCESSION NUMBER 9804 FOR 2-O-SULFO-ALPHA-L- REMARK 3 IDOPYRANURONIC ACID (IDS OR IDOA2S) AND 9778 FOR N,O6-DISULFO- REMARK 3 GLUCOSAMINE (SGN OR GLCNS6S). THE GLOBALLY FLEXIBLE DOCKING REMARK 3 SIMULATIONS REQUIRED THE PROMMP-7 POLYPEPTIDE TO BE LINKED TO THE REMARK 3 CALCIUM AND ZINC IONS AND HEPARIN DP8 CHAINS VIA TETHERS OF NON- REMARK 3 INTERACTING PSEUDOATOMS. WITH THIS TETHERING AND FLEXIBLE REMARK 3 STRUCTURAL INTEGRITY ENFORCED, THE CARBOHYDRATE CHAINS WERE DOCKED REMARK 3 WITH THE INTERMOLECULAR DISTANCE RESTRAINTS REMARK 4 REMARK 4 5UE5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-JAN-17. REMARK 100 THE DEPOSITION ID IS D_1000225723. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 310; 310; 310; 310 REMARK 210 PH : 6.6; 6.6; 6.6; 6.6 REMARK 210 IONIC STRENGTH : 180; 180; 180; 30 REMARK 210 PRESSURE : 1 ATM; 1 ATM; 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 300 UM [U-99% 15N] PROMMP-7, 450 REMARK 210 UM HEPARIN DP8, 93% H2O/7% D2O; REMARK 210 300 UM [U-99% 2H/15N] PROMMP-7, REMARK 210 450 UM HEPARIN DP8-TEMPO, 93% REMARK 210 H2O/7% D2O; 300 UM [U-99% 2H/15N] REMARK 210 PROMMP-7, 450 UM HEPARIN DP8, REMARK 210 93% H2O/7% D2O; 300 UM [U-99% 2H/ REMARK 210 15N] PROMMP-7, 450 UM HEPARIN REMARK 210 DP4, 93% H2O/7% D2O; 300 UM [U- REMARK 210 100% 13C; U-100% 15N; U-80% 2H] REMARK 210 PROMMP-7, 93% H2O/7% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D 1H-15N NOESY; TROSY-DETECTED REMARK 210 TITRATION; PRES BY PROJECT-CPMG REMARK 210 TROSY; SOLVENT PRES, 1H REMARK 210 RELAXATION DETECTED VIA TROSY; REMARK 210 3D HNCACB; 3D CBCA(CO)NH REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA 2.1, SPARKY, ANALYSIS, REMARK 210 TOPSPIN REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 16 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 4 HIS A 143 CE1 HIS A 143 NE2 -0.067 REMARK 500 6 HIS A 143 CE1 HIS A 143 NE2 -0.067 REMARK 500 8 HIS A 123 CE1 HIS A 123 NE2 -0.067 REMARK 500 13 HIS A 198 CE1 HIS A 198 NE2 -0.067 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 1 TRP A 12 CE2 - CD2 - CG ANGL. DEV. = -4.8 DEGREES REMARK 500 1 ARG A 21 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 TRP A 84 CE2 - CD2 - CG ANGL. DEV. = -4.9 DEGREES REMARK 500 1 ARG A 92 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 ARG A 98 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 ARG A 107 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 TRP A 116 CE2 - CD2 - CG ANGL. DEV. = -4.8 DEGREES REMARK 500 1 ARG A 125 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 1 ARG A 177 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 TRP A 178 CE2 - CD2 - CG ANGL. DEV. = -4.9 DEGREES REMARK 500 1 ARG A 241 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 ARG A 245 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 2 TRP A 12 CE2 - CD2 - CG ANGL. DEV. = -4.8 DEGREES REMARK 500 2 ARG A 92 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 2 ARG A 107 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 TRP A 116 CE2 - CD2 - CG ANGL. DEV. = -5.2 DEGREES REMARK 500 2 ARG A 125 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 2 TRP A 129 CE2 - CD2 - CG ANGL. DEV. = -5.0 DEGREES REMARK 500 2 TRP A 178 CE2 - CD2 - CG ANGL. DEV. = -5.3 DEGREES REMARK 500 2 ARG A 245 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 3 TRP A 12 CE2 - CD2 - CG ANGL. DEV. = -4.9 DEGREES REMARK 500 3 ARG A 21 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 3 ARG A 57 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 3 TRP A 84 CE2 - CD2 - CG ANGL. DEV. = -5.0 DEGREES REMARK 500 3 TRP A 116 CE2 - CD2 - CG ANGL. DEV. = -5.2 DEGREES REMARK 500 3 ARG A 125 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 3 TRP A 129 CE2 - CD2 - CG ANGL. DEV. = -4.8 DEGREES REMARK 500 3 TRP A 178 CE2 - CD2 - CG ANGL. DEV. = -5.0 DEGREES REMARK 500 3 HIS A 198 CG - CD2 - NE2 ANGL. DEV. = -8.0 DEGREES REMARK 500 3 ARG A 241 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 3 ARG A 245 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 4 ARG A 21 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 4 TRP A 84 CE2 - CD2 - CG ANGL. DEV. = -5.2 DEGREES REMARK 500 4 ARG A 98 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 4 ARG A 107 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 4 TRP A 116 CE2 - CD2 - CG ANGL. DEV. = -4.8 DEGREES REMARK 500 4 ARG A 125 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 4 ARG A 177 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 4 TRP A 178 CE2 - CD2 - CG ANGL. DEV. = -4.8 DEGREES REMARK 500 4 ARG A 245 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 5 ARG A 21 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 5 TYR A 23 CB - CG - CD2 ANGL. DEV. = -3.6 DEGREES REMARK 500 5 ARG A 57 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 5 ARG A 66 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 5 ARG A 92 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 5 ARG A 98 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 5 ARG A 125 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 5 TRP A 178 CE2 - CD2 - CG ANGL. DEV. = -5.1 DEGREES REMARK 500 5 ARG A 245 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 6 TRP A 12 CE2 - CD2 - CG ANGL. DEV. = -4.9 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 153 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 1 LEU A 24 146.11 68.63 REMARK 500 1 THR A 29 47.38 -104.46 REMARK 500 1 LEU A 48 137.06 -34.66 REMARK 500 1 ILE A 50 95.51 -68.16 REMARK 500 1 LEU A 54 81.69 -151.48 REMARK 500 1 ASN A 55 -50.68 -175.63 REMARK 500 1 SER A 56 -103.42 -78.01 REMARK 500 1 ARG A 66 -57.06 -165.46 REMARK 500 1 GLU A 74 81.03 -161.60 REMARK 500 1 SER A 81 152.08 63.98 REMARK 500 1 TRP A 84 100.18 -54.99 REMARK 500 1 ALA A 112 -60.63 -91.05 REMARK 500 1 TRP A 129 97.97 -172.76 REMARK 500 1 ALA A 142 20.11 -79.21 REMARK 500 1 TYR A 147 127.32 82.31 REMARK 500 1 ASP A 150 -57.21 77.43 REMARK 500 1 ASN A 154 150.06 -29.37 REMARK 500 1 THR A 155 98.14 70.69 REMARK 500 1 PRO A 162 81.22 -69.71 REMARK 500 1 THR A 164 171.83 61.11 REMARK 500 1 ASP A 173 107.60 -57.76 REMARK 500 1 LEU A 184 -63.29 -132.70 REMARK 500 1 MET A 212 39.11 -99.47 REMARK 500 1 ASN A 218 -176.17 57.62 REMARK 500 1 PHE A 224 140.62 71.30 REMARK 500 1 SER A 244 -77.07 57.06 REMARK 500 1 ARG A 245 80.32 50.92 REMARK 500 2 GLN A 2 36.94 -153.81 REMARK 500 2 LEU A 24 159.10 66.14 REMARK 500 2 THR A 29 42.30 -100.82 REMARK 500 2 ASN A 55 -54.46 166.35 REMARK 500 2 SER A 56 -94.03 -85.48 REMARK 500 2 ARG A 66 -58.40 -163.70 REMARK 500 2 TYR A 75 170.41 60.04 REMARK 500 2 SER A 76 130.57 70.90 REMARK 500 2 SER A 81 151.01 61.80 REMARK 500 2 GLU A 119 33.12 -93.90 REMARK 500 2 LEU A 122 161.44 -47.52 REMARK 500 2 TRP A 129 97.56 -165.62 REMARK 500 2 ALA A 142 34.07 -80.46 REMARK 500 2 TYR A 147 126.10 77.03 REMARK 500 2 ASP A 150 5.04 52.01 REMARK 500 2 ASN A 154 139.69 -27.20 REMARK 500 2 THR A 155 120.85 75.52 REMARK 500 2 PRO A 162 74.03 -67.50 REMARK 500 2 ASP A 173 105.72 -57.73 REMARK 500 2 ASP A 180 -63.67 -131.81 REMARK 500 2 MET A 212 49.04 -100.63 REMARK 500 2 THR A 215 41.56 -89.05 REMARK 500 2 PHE A 224 130.90 -33.11 REMARK 500 REMARK 500 THIS ENTRY HAS 433 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 TYR A 216 0.08 SIDE CHAIN REMARK 500 2 TYR A 23 0.10 SIDE CHAIN REMARK 500 3 TYR A 147 0.11 SIDE CHAIN REMARK 500 4 PHE A 160 0.11 SIDE CHAIN REMARK 500 4 TYR A 213 0.13 SIDE CHAIN REMARK 500 4 TYR A 216 0.08 SIDE CHAIN REMARK 500 5 TYR A 91 0.11 SIDE CHAIN REMARK 500 5 TYR A 216 0.16 SIDE CHAIN REMARK 500 6 TYR A 213 0.10 SIDE CHAIN REMARK 500 6 TYR A 216 0.20 SIDE CHAIN REMARK 500 7 TYR A 216 0.06 SIDE CHAIN REMARK 500 8 TYR A 213 0.12 SIDE CHAIN REMARK 500 9 TYR A 23 0.14 SIDE CHAIN REMARK 500 12 TYR A 18 0.13 SIDE CHAIN REMARK 500 12 TYR A 23 0.09 SIDE CHAIN REMARK 500 12 TYR A 213 0.09 SIDE CHAIN REMARK 500 12 TYR A 216 0.09 SIDE CHAIN REMARK 500 14 TYR A 213 0.10 SIDE CHAIN REMARK 500 16 TYR A 216 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 1 SGN B 1 REMARK 610 2 SGN B 1 REMARK 610 3 SGN B 1 REMARK 610 4 SGN B 1 REMARK 610 5 SGN B 1 REMARK 610 6 SGN B 1 REMARK 610 7 SGN B 1 REMARK 610 8 SGN B 1 REMARK 610 9 SGN B 1 REMARK 610 10 SGN B 1 REMARK 610 11 SGN B 1 REMARK 610 12 SGN B 1 REMARK 610 13 SGN B 1 REMARK 610 14 SGN B 1 REMARK 610 15 SGN B 1 REMARK 610 16 SGN B 1 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 304 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 67 SG REMARK 620 2 HIS A 194 NE2 79.1 REMARK 620 3 HIS A 198 NE2 98.4 83.9 REMARK 620 4 HIS A 204 NE2 154.3 98.3 106.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 301 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 133 O REMARK 620 2 GLY A 165 O 104.1 REMARK 620 3 LEU A 166 O 159.1 85.0 REMARK 620 4 GLY A 167 O 130.3 78.6 69.5 REMARK 620 5 ASP A 169 OD1 77.1 146.3 84.9 126.9 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 303 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 143 NE2 REMARK 620 2 ASP A 145 OD2 74.2 REMARK 620 3 HIS A 158 NE2 145.3 120.2 REMARK 620 4 HIS A 171 ND1 98.3 172.1 67.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 302 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 150 OD1 REMARK 620 2 ASP A 150 OD2 49.2 REMARK 620 3 GLY A 151 O 59.7 73.8 REMARK 620 4 GLY A 153 O 83.2 120.6 115.1 REMARK 620 5 ASN A 154 O 51.5 72.6 109.9 48.6 REMARK 620 6 THR A 155 O 95.8 73.4 147.1 80.0 56.8 REMARK 620 7 ASP A 173 OD2 104.8 64.9 71.8 171.6 135.2 96.6 REMARK 620 8 GLU A 176 OE2 127.9 175.8 102.2 59.7 108.2 110.5 115.3 REMARK 620 N 1 2 3 4 5 6 7 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2MZE RELATED DB: PDB REMARK 900 THE FREE STATE OF THIS ZYMOGEN PROTEASE REMARK 900 RELATED ID: 5UE2 RELATED DB: PDB REMARK 900 ANOTHER COMPLEX THAT THE HEPARIN OCTASACCHARIDE FORMS WITH THIS REMARK 900 ZYMOGEN REMARK 900 RELATED ID: 25485 RELATED DB: BMRB DBREF 5UE5 A 1 247 UNP P09237 MMP7_HUMAN 21 267 SEQADV 5UE5 ALA A 195 UNP P09237 GLU 215 CONFLICT SEQRES 1 A 247 PRO GLN GLU ALA GLY GLY MET SER GLU LEU GLN TRP GLU SEQRES 2 A 247 GLN ALA GLN ASP TYR LEU LYS ARG PHE TYR LEU TYR ASP SEQRES 3 A 247 SER GLU THR LYS ASN ALA ASN SER LEU GLU ALA LYS LEU SEQRES 4 A 247 LYS GLU MET GLN LYS PHE PHE GLY LEU PRO ILE THR GLY SEQRES 5 A 247 MET LEU ASN SER ARG VAL ILE GLU ILE MET GLN LYS PRO SEQRES 6 A 247 ARG CYS GLY VAL PRO ASP VAL ALA GLU TYR SER LEU PHE SEQRES 7 A 247 PRO ASN SER PRO LYS TRP THR SER LYS VAL VAL THR TYR SEQRES 8 A 247 ARG ILE VAL SER TYR THR ARG ASP LEU PRO HIS ILE THR SEQRES 9 A 247 VAL ASP ARG LEU VAL SER LYS ALA LEU ASN MET TRP GLY SEQRES 10 A 247 LYS GLU ILE PRO LEU HIS PHE ARG LYS VAL VAL TRP GLY SEQRES 11 A 247 THR ALA ASP ILE MET ILE GLY PHE ALA ARG GLY ALA HIS SEQRES 12 A 247 GLY ASP SER TYR PRO PHE ASP GLY PRO GLY ASN THR LEU SEQRES 13 A 247 ALA HIS ALA PHE ALA PRO GLY THR GLY LEU GLY GLY ASP SEQRES 14 A 247 ALA HIS PHE ASP GLU ASP GLU ARG TRP THR ASP GLY SER SEQRES 15 A 247 SER LEU GLY ILE ASN PHE LEU TYR ALA ALA THR HIS ALA SEQRES 16 A 247 LEU GLY HIS SER LEU GLY MET GLY HIS SER SER ASP PRO SEQRES 17 A 247 ASN ALA VAL MET TYR PRO THR TYR GLY ASN GLY ASP PRO SEQRES 18 A 247 GLN ASN PHE LYS LEU SER GLN ASP ASP ILE LYS GLY ILE SEQRES 19 A 247 GLN LYS LEU TYR GLY LYS ARG SER ASN SER ARG LYS LYS HET SGN B 1 28 HET IDS B 2 22 HET SGN B 3 28 HET IDS B 4 22 HET SGN B 5 28 HET IDS B 6 22 HET SGN B 7 28 HET IDS B 8 22 HET CA A 301 1 HET CA A 302 1 HET ZN A 303 1 HET ZN A 304 1 HETNAM SGN 2-DEOXY-6-O-SULFO-2-(SULFOAMINO)-ALPHA-D-GLUCOPYRANOSE HETNAM IDS 2-O-SULFO-ALPHA-L-IDOPYRANURONIC ACID HETNAM CA CALCIUM ION HETNAM ZN ZINC ION HETSYN SGN N,O6-DISULFO-GLUCOSAMINE; 6-O-SULFO-N-SULFO-ALPHA-D- HETSYN 2 SGN GLUCOSAMINE; 2-DEOXY-6-O-SULFO-2-(SULFOAMINO)-ALPHA-D- HETSYN 3 SGN GLUCOSE; 2-DEOXY-6-O-SULFO-2-(SULFOAMINO)-D-GLUCOSE; HETSYN 4 SGN 2-DEOXY-6-O-SULFO-2-(SULFOAMINO)-GLUCOSE HETSYN IDS O2-SULFO-GLUCURONIC ACID; 2-O-SULFO-ALPHA-L-IDURONIC HETSYN 2 IDS ACID; 2-O-SULFO-L-IDURONIC ACID; 2-O-SULFO-IDURONIC HETSYN 3 IDS ACID FORMUL 2 SGN 4(C6 H13 N O11 S2) FORMUL 2 IDS 4(C6 H10 O10 S) FORMUL 3 CA 2(CA 2+) FORMUL 5 ZN 2(ZN 2+) HELIX 1 AA1 GLU A 3 MET A 7 5 5 HELIX 2 AA2 SER A 8 TYR A 23 1 16 HELIX 3 AA3 ASP A 26 LYS A 30 5 5 HELIX 4 AA4 ASN A 33 GLY A 47 1 15 HELIX 5 AA5 SER A 56 LYS A 64 1 9 HELIX 6 AA6 PRO A 101 GLU A 119 1 19 HELIX 7 AA7 ARG A 140 GLY A 144 5 5 HELIX 8 AA8 PHE A 188 LEU A 200 1 13 HELIX 9 AA9 SER A 227 GLY A 239 1 13 SHEET 1 AA1 2 VAL A 88 VAL A 89 0 SHEET 2 AA1 2 HIS A 123 PHE A 124 1 O HIS A 123 N VAL A 89 SHEET 1 AA2 3 TYR A 91 ILE A 93 0 SHEET 2 AA2 3 ILE A 134 ALA A 139 1 O ILE A 136 N ARG A 92 SHEET 3 AA2 3 ALA A 170 ASP A 173 1 O ALA A 170 N MET A 135 SHEET 1 AA3 2 TRP A 178 THR A 179 0 SHEET 2 AA3 2 ILE A 186 ASN A 187 1 O ILE A 186 N THR A 179 LINK O4 SGN B 1 C1 IDS B 2 1555 1555 1.46 LINK O4 IDS B 2 C1 SGN B 3 1555 1555 1.46 LINK O4 SGN B 3 C1 IDS B 4 1555 1555 1.46 LINK O4 IDS B 4 C1 SGN B 5 1555 1555 1.45 LINK O4 SGN B 5 C1 IDS B 6 1555 1555 1.46 LINK O4 IDS B 6 C1 SGN B 7 1555 1555 1.45 LINK O4 SGN B 7 C1 IDS B 8 1555 1555 1.45 LINK SG CYS A 67 ZN ZN A 304 1555 1555 2.50 LINK O ASP A 133 CA CA A 301 1555 1555 2.40 LINK NE2 HIS A 143 ZN ZN A 303 1555 1555 2.26 LINK OD2 ASP A 145 ZN ZN A 303 1555 1555 2.26 LINK OD1 ASP A 150 CA CA A 302 1555 1555 2.70 LINK OD2 ASP A 150 CA CA A 302 1555 1555 2.62 LINK O GLY A 151 CA CA A 302 1555 1555 2.42 LINK O GLY A 153 CA CA A 302 1555 1555 2.72 LINK O ASN A 154 CA CA A 302 1555 1555 3.17 LINK O THR A 155 CA CA A 302 1555 1555 2.42 LINK NE2 HIS A 158 ZN ZN A 303 1555 1555 2.26 LINK O GLY A 165 CA CA A 301 1555 1555 2.41 LINK O LEU A 166 CA CA A 301 1555 1555 2.41 LINK O GLY A 167 CA CA A 301 1555 1555 2.59 LINK OD1 ASP A 169 CA CA A 301 1555 1555 2.41 LINK ND1 HIS A 171 ZN ZN A 303 1555 1555 2.46 LINK OD2 ASP A 173 CA CA A 302 1555 1555 2.44 LINK OE2 GLU A 176 CA CA A 302 1555 1555 2.42 LINK NE2 HIS A 194 ZN ZN A 304 1555 1555 2.28 LINK NE2 HIS A 198 ZN ZN A 304 1555 1555 2.24 LINK NE2 HIS A 204 ZN ZN A 304 1555 1555 2.28 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1