1ITU - Header Asymmetric Unit

HEADER HYDROLASE 03-FEB-02 1ITU

TITLE HUMAN RENAL DIPEPTIDASE COMPLEXED WITH CILASTATIN

COMPND MOL_ID: 1; COMPND 2 MOLECULE: RENAL DIPEPTIDASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: MICROSOMAL DIPEPTIDASE; COMPND 5 EC: 3.4.13.19; COMPND 6 ENGINEERED: YES

SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 TISSUE: RENAL CORTEX; SOURCE 6 EXPRESSION_SYSTEM: PICHIA PASTORIS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 4922; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: GS115; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PHILD2

KEYWDS DIPEPTIDASE, GLYCOPROTEIN, MEMBRANE-BOUND, ZINC PROTEASE BETA- KEYWDS 2 LACTAMASE, CILASTATIN, COMPLEX (HYDROLASE-INHIBITOR), HYDROLASE

EXPDTA X-RAY DIFFRACTION

AUTHOR Y.NITANAI,Y.SATOW,H.ADACHI,M.TSUJIMOTO

REVDAT 3 13-JUL-11 1ITU 1 VERSN REVDAT 2 24-FEB-09 1ITU 1 VERSN REVDAT 1 28-AUG-02 1ITU 0

JRNL AUTH Y.NITANAI,Y.SATOW,H.ADACHI,M.TSUJIMOTO JRNL TITL CRYSTAL STRUCTURE OF HUMAN RENAL DIPEPTIDASE INVOLVED IN JRNL TITL 2 BETA-LACTAM HYDROLYSIS JRNL REF J.MOL.BIOL. V. 321 177 2002 JRNL REFN ISSN 0022-2836 JRNL PMID 12144777 JRNL DOI 10.1016/S0022-2836(02)00632-0

REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH Y.NITANAI,Y.SATOW,H.ADACHI,M.TSUJIMOTO REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY X-RAY INVESTIGATION OF A REMARK 1 TITL 2 GLYCOPROTEIN, HUMAN RENAL DIPEPTIDASE REMARK 1 REF J.CRYST.GROWTH V. 168 280 1996 REMARK 1 REFN ISSN 0022-0248 REMARK 1 DOI 10.1016/0022-0248(96)00332-6

REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS.

REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.843 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1000000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0010 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 95.5 REMARK 3 NUMBER OF REFLECTIONS : 45648 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) : 0.185 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4590 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 15 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 82.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2357 REMARK 3 BIN R VALUE (WORKING SET) : 0.2875 REMARK 3 BIN FREE R VALUE : 0.3484 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 285 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5776 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 92 REMARK 3 SOLVENT ATOMS : 607 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.19 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.22 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.20 REMARK 3 ESD FROM SIGMAA (A) : 0.23 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) : 0.29 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.26 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.46 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.76 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.36 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) : 1.874 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.669 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.059 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.320 ; 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 : PARHCSDX.PRO REMARK 3 PARAMETER FILE 2 : PARAM19X.SOL REMARK 3 PARAMETER FILE 3 : PARAM3.CHO REMARK 3 PARAMETER FILE 4 : PARAMETER.ELEMENTS REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : TOPH19.SOL REMARK 3 TOPOLOGY FILE 3 : TOPH3.CHO REMARK 3 TOPOLOGY FILE 4 : TOPOLOGY.ELEMENTS REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL

REMARK 4 REMARK 4 1ITU COMPLIES WITH FORMAT V. 3.15, 01-DEC-08

REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-FEB-02. REMARK 100 THE RCSB ID CODE IS RCSB005267.

REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-NOV-96 REMARK 200 TEMPERATURE (KELVIN) : 120 REMARK 200 PH : 7.6 REMARK 200 NUMBER OF CRYSTALS USED : 3 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU300 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 46290 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 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 (%) : 96.1 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.08700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 84.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.27400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR 3.843 REMARK 200 STARTING MODEL: NATIVE DIPEPTIDASE STRUCTURE REMARK 200 REMARK 200 REMARK: NULL

REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8000, HEPES, PH 7.6, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 283.0K

REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 39.74550 REMARK 290 SMTRY3 2 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 BIOLOGICAL ASSEMBLY IS A DIMER GENERATED FROM THE DIMER 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6430 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24390 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -155.0 KCAL/MOL 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 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 PHE A 217 N - CA - C ANGL. DEV. = -17.1 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 20 109.67 -163.67 REMARK 500 ASP A 22 33.61 -88.40 REMARK 500 LYS A 76 -106.99 -131.96 REMARK 500 HIS A 152 -133.19 -105.34 REMARK 500 SER A 153 48.86 -96.23 REMARK 500 HIS A 219 74.94 -162.46 REMARK 500 SER A 221 -165.11 -112.54 REMARK 500 ILE A 256 -63.09 -94.70 REMARK 500 ALA A 327 -43.56 -138.09 REMARK 500 SER A 368 88.49 93.33 REMARK 500 HIS B 20 109.78 -165.77 REMARK 500 ASP B 22 37.69 -95.88 REMARK 500 LYS B 76 -108.46 -135.83 REMARK 500 HIS B 152 -138.14 -103.00 REMARK 500 SER B 153 45.26 -89.60 REMARK 500 HIS B 198 -4.61 68.85 REMARK 500 HIS B 219 72.43 -162.54 REMARK 500 SER B 221 -166.14 -111.03 REMARK 500 ARG B 229 1.02 -68.85 REMARK 500 ALA B 327 -30.94 -150.09 REMARK 500 SER B 368 -66.53 -151.93 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 ASP A 328 24.7 L L OUTSIDE RANGE 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 A1409 DISTANCE = 5.13 ANGSTROMS REMARK 525 HOH A1469 DISTANCE = 5.21 ANGSTROMS REMARK 525 HOH A1554 DISTANCE = 5.42 ANGSTROMS REMARK 525 HOH A1604 DISTANCE = 6.98 ANGSTROMS REMARK 525 HOH A1605 DISTANCE = 5.31 ANGSTROMS REMARK 525 HOH B1557 DISTANCE = 5.02 ANGSTROMS REMARK 525 HOH B1560 DISTANCE = 5.22 ANGSTROMS REMARK 525 HOH B1597 DISTANCE = 5.43 ANGSTROMS

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 CIL A 451 REMARK 610 CIL B 452

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 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 20 NE2 REMARK 620 2 ASP A 22 OD1 105.8 REMARK 620 3 GLU A 125 OE1 95.3 141.8 REMARK 620 4 HOH A 421 O 101.7 90.2 116.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 402 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 125 OE2 REMARK 620 2 HIS A 219 NE2 89.3 REMARK 620 3 HIS A 198 NE2 82.9 104.1 REMARK 620 4 CIL A 451 O13 168.1 94.7 85.2 REMARK 620 5 HOH A 421 O 110.5 98.4 154.0 80.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 411 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 20 NE2 REMARK 620 2 ASP B 22 OD1 106.3 REMARK 620 3 GLU B 125 OE1 93.0 141.5 REMARK 620 4 HOH B 422 O 104.8 91.3 116.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 412 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 125 OE2 REMARK 620 2 HIS B 219 NE2 85.7 REMARK 620 3 HIS B 198 NE2 87.0 107.4 REMARK 620 4 HOH B 422 O 110.5 97.8 150.5 REMARK 620 5 CIL B 452 O13 170.0 98.8 83.2 77.9 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 NAG A 461 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAG B 462 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAG A 463 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAG B 464 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 411 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 412 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CIL A 451 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CIL B 452

REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1ITQ RELATED DB: PDB REMARK 900 1ITQ CONTAINS THE SAME PROTEIN WITHOUT A LIGAND.

DBREF 1ITU A 1 369 UNP P16444 MDP1_HUMAN 17 385 DBREF 1ITU B 1 369 UNP P16444 MDP1_HUMAN 17 385

SEQRES 1 A 369 ASP PHE PHE ARG ASP GLU ALA GLU ARG ILE MET ARG ASP SEQRES 2 A 369 SER PRO VAL ILE ASP GLY HIS ASN ASP LEU PRO TRP GLN SEQRES 3 A 369 LEU LEU ASP MET PHE ASN ASN ARG LEU GLN ASP GLU ARG SEQRES 4 A 369 ALA ASN LEU THR THR LEU ALA GLY THR HIS THR ASN ILE SEQRES 5 A 369 PRO LYS LEU ARG ALA GLY PHE VAL GLY GLY GLN PHE TRP SEQRES 6 A 369 SER VAL TYR THR PRO CYS ASP THR GLN ASN LYS ASP ALA SEQRES 7 A 369 VAL ARG ARG THR LEU GLU GLN MET ASP VAL VAL HIS ARG SEQRES 8 A 369 MET CYS ARG MET TYR PRO GLU THR PHE LEU TYR VAL THR SEQRES 9 A 369 SER SER ALA GLY ILE ARG GLN ALA PHE ARG GLU GLY LYS SEQRES 10 A 369 VAL ALA SER LEU ILE GLY VAL GLU GLY GLY HIS SER ILE SEQRES 11 A 369 ASP SER SER LEU GLY VAL LEU ARG ALA LEU TYR GLN LEU SEQRES 12 A 369 GLY MET ARG TYR LEU THR LEU THR HIS SER CYS ASN THR SEQRES 13 A 369 PRO TRP ALA ASP ASN TRP LEU VAL ASP THR GLY ASP SER SEQRES 14 A 369 GLU PRO GLN SER GLN GLY LEU SER PRO PHE GLY GLN ARG SEQRES 15 A 369 VAL VAL LYS GLU LEU ASN ARG LEU GLY VAL LEU ILE ASP SEQRES 16 A 369 LEU ALA HIS VAL SER VAL ALA THR MET LYS ALA THR LEU SEQRES 17 A 369 GLN LEU SER ARG ALA PRO VAL ILE PHE SER HIS SER SER SEQRES 18 A 369 ALA TYR SER VAL CYS ALA SER ARG ARG ASN VAL PRO ASP SEQRES 19 A 369 ASP VAL LEU ARG LEU VAL LYS GLN THR ASP SER LEU VAL SEQRES 20 A 369 MET VAL ASN PHE TYR ASN ASN TYR ILE SER CYS THR ASN SEQRES 21 A 369 LYS ALA ASN LEU SER GLN VAL ALA ASP HIS LEU ASP HIS SEQRES 22 A 369 ILE LYS GLU VAL ALA GLY ALA ARG ALA VAL GLY PHE GLY SEQRES 23 A 369 GLY ASP PHE ASP GLY VAL PRO ARG VAL PRO GLU GLY LEU SEQRES 24 A 369 GLU ASP VAL SER LYS TYR PRO ASP LEU ILE ALA GLU LEU SEQRES 25 A 369 LEU ARG ARG ASN TRP THR GLU ALA GLU VAL LYS GLY ALA SEQRES 26 A 369 LEU ALA ASP ASN LEU LEU ARG VAL PHE GLU ALA VAL GLU SEQRES 27 A 369 GLN ALA SER ASN LEU THR GLN ALA PRO GLU GLU GLU PRO SEQRES 28 A 369 ILE PRO LEU ASP GLN LEU GLY GLY SER CYS ARG THR HIS SEQRES 29 A 369 TYR GLY TYR SER SER SEQRES 1 B 369 ASP PHE PHE ARG ASP GLU ALA GLU ARG ILE MET ARG ASP SEQRES 2 B 369 SER PRO VAL ILE ASP GLY HIS ASN ASP LEU PRO TRP GLN SEQRES 3 B 369 LEU LEU ASP MET PHE ASN ASN ARG LEU GLN ASP GLU ARG SEQRES 4 B 369 ALA ASN LEU THR THR LEU ALA GLY THR HIS THR ASN ILE SEQRES 5 B 369 PRO LYS LEU ARG ALA GLY PHE VAL GLY GLY GLN PHE TRP SEQRES 6 B 369 SER VAL TYR THR PRO CYS ASP THR GLN ASN LYS ASP ALA SEQRES 7 B 369 VAL ARG ARG THR LEU GLU GLN MET ASP VAL VAL HIS ARG SEQRES 8 B 369 MET CYS ARG MET TYR PRO GLU THR PHE LEU TYR VAL THR SEQRES 9 B 369 SER SER ALA GLY ILE ARG GLN ALA PHE ARG GLU GLY LYS SEQRES 10 B 369 VAL ALA SER LEU ILE GLY VAL GLU GLY GLY HIS SER ILE SEQRES 11 B 369 ASP SER SER LEU GLY VAL LEU ARG ALA LEU TYR GLN LEU SEQRES 12 B 369 GLY MET ARG TYR LEU THR LEU THR HIS SER CYS ASN THR SEQRES 13 B 369 PRO TRP ALA ASP ASN TRP LEU VAL ASP THR GLY ASP SER SEQRES 14 B 369 GLU PRO GLN SER GLN GLY LEU SER PRO PHE GLY GLN ARG SEQRES 15 B 369 VAL VAL LYS GLU LEU ASN ARG LEU GLY VAL LEU ILE ASP SEQRES 16 B 369 LEU ALA HIS VAL SER VAL ALA THR MET LYS ALA THR LEU SEQRES 17 B 369 GLN LEU SER ARG ALA PRO VAL ILE PHE SER HIS SER SER SEQRES 18 B 369 ALA TYR SER VAL CYS ALA SER ARG ARG ASN VAL PRO ASP SEQRES 19 B 369 ASP VAL LEU ARG LEU VAL LYS GLN THR ASP SER LEU VAL SEQRES 20 B 369 MET VAL ASN PHE TYR ASN ASN TYR ILE SER CYS THR ASN SEQRES 21 B 369 LYS ALA ASN LEU SER GLN VAL ALA ASP HIS LEU ASP HIS SEQRES 22 B 369 ILE LYS GLU VAL ALA GLY ALA ARG ALA VAL GLY PHE GLY SEQRES 23 B 369 GLY ASP PHE ASP GLY VAL PRO ARG VAL PRO GLU GLY LEU SEQRES 24 B 369 GLU ASP VAL SER LYS TYR PRO ASP LEU ILE ALA GLU LEU SEQRES 25 B 369 LEU ARG ARG ASN TRP THR GLU ALA GLU VAL LYS GLY ALA SEQRES 26 B 369 LEU ALA ASP ASN LEU LEU ARG VAL PHE GLU ALA VAL GLU SEQRES 27 B 369 GLN ALA SER ASN LEU THR GLN ALA PRO GLU GLU GLU PRO SEQRES 28 B 369 ILE PRO LEU ASP GLN LEU GLY GLY SER CYS ARG THR HIS SEQRES 29 B 369 TYR GLY TYR SER SER

MODRES 1ITU ASN A 41 ASN GLYCOSYLATION SITE MODRES 1ITU ASN A 316 ASN GLYCOSYLATION SITE MODRES 1ITU ASN B 41 ASN GLYCOSYLATION SITE MODRES 1ITU ASN B 316 ASN GLYCOSYLATION SITE

HET NAG A 461 14 HET NAG B 462 14 HET NAG A 463 14 HET NAG B 464 14 HET ZN A 401 1 HET ZN A 402 1 HET ZN B 411 1 HET ZN B 412 1 HET CIL A 451 16 HET CIL B 452 16

HETNAM NAG N-ACETYL-D-GLUCOSAMINE HETNAM ZN ZINC ION HETNAM CIL CILASTATIN

FORMUL 3 NAG 4(C8 H15 N O6) FORMUL 7 ZN 4(ZN 2+) FORMUL 11 CIL 2(C16 H26 N2 O5 S) FORMUL 13 HOH *607(H2 O)

HELIX 1 1 ASP A 1 ARG A 12 1 12 HELIX 2 2 ASP A 22 ASN A 32 1 11 HELIX 3 3 ASP A 37 ASN A 41 5 5 HELIX 4 4 ASN A 51 GLY A 58 1 8 HELIX 5 5 PRO A 70 GLN A 74 5 5 HELIX 6 6 ASP A 77 TYR A 96 1 20 HELIX 7 7 SER A 105 GLY A 116 1 12 HELIX 8 8 GLY A 127 ASP A 131 5 5 HELIX 9 9 SER A 133 LEU A 143 1 11 HELIX 10 10 ASN A 161 ASP A 165 5 5 HELIX 11 11 SER A 177 GLY A 191 1 15 HELIX 12 12 SER A 200 SER A 211 1 12 HELIX 13 13 PRO A 233 ASP A 244 1 12 HELIX 14 14 TYR A 252 SER A 257 1 6 HELIX 15 15 ASN A 263 GLY A 279 1 17 HELIX 16 16 LYS A 304 ARG A 315 1 12 HELIX 17 17 THR A 318 ALA A 327 1 10 HELIX 18 18 ALA A 327 SER A 341 1 15 HELIX 19 19 PRO A 353 LEU A 357 5 5 HELIX 20 20 ASP B 1 SER B 14 1 14 HELIX 21 21 ASP B 22 ASN B 32 1 11 HELIX 22 22 ASP B 37 ASN B 41 5 5 HELIX 23 23 ASN B 51 GLY B 58 1 8 HELIX 24 24 PRO B 70 GLN B 74 5 5 HELIX 25 25 ASP B 77 TYR B 96 1 20 HELIX 26 26 SER B 105 GLY B 116 1 12 HELIX 27 27 GLY B 127 ILE B 130 5 4 HELIX 28 28 SER B 133 LEU B 143 1 11 HELIX 29 29 ASN B 161 ASP B 165 5 5 HELIX 30 30 SER B 177 GLY B 191 1 15 HELIX 31 31 SER B 200 SER B 211 1 12 HELIX 32 32 PRO B 233 ASP B 244 1 12 HELIX 33 33 TYR B 252 SER B 257 1 6 HELIX 34 34 ASN B 263 ALA B 278 1 16 HELIX 35 35 GLY B 279 ARG B 281 5 3 HELIX 36 36 ASP B 301 SER B 303 5 3 HELIX 37 37 LYS B 304 ARG B 315 1 12 HELIX 38 38 THR B 318 ALA B 327 1 10 HELIX 39 39 ALA B 327 ALA B 340 1 14 HELIX 40 40 PRO B 353 LEU B 357 5 5

SHEET 1 A 4 VAL A 16 ASN A 21 0 SHEET 2 A 4 VAL A 60 VAL A 67 1 O SER A 66 N ASN A 21 SHEET 3 A 4 VAL A 118 GLU A 125 1 O LEU A 121 N GLN A 63 SHEET 4 A 4 PHE A 100 TYR A 102 1 N LEU A 101 O SER A 120 SHEET 1 B 5 VAL A 16 ASN A 21 0 SHEET 2 B 5 VAL A 60 VAL A 67 1 O SER A 66 N ASN A 21 SHEET 3 B 5 VAL A 118 GLU A 125 1 O LEU A 121 N GLN A 63 SHEET 4 B 5 MET A 145 THR A 149 1 O THR A 149 N VAL A 124 SHEET 5 B 5 LEU A 193 ASP A 195 1 O ASP A 195 N LEU A 148 SHEET 1 C 3 ILE A 216 PHE A 217 0 SHEET 2 C 3 LEU A 246 VAL A 249 1 O MET A 248 N PHE A 217 SHEET 3 C 3 VAL A 283 PHE A 285 1 O GLY A 284 N VAL A 249 SHEET 1 D 4 VAL B 16 ASN B 21 0 SHEET 2 D 4 VAL B 60 VAL B 67 1 O SER B 66 N ASN B 21 SHEET 3 D 4 VAL B 118 GLU B 125 1 O GLY B 123 N VAL B 67 SHEET 4 D 4 PHE B 100 TYR B 102 1 N LEU B 101 O SER B 120 SHEET 1 E 5 VAL B 16 ASN B 21 0 SHEET 2 E 5 VAL B 60 VAL B 67 1 O SER B 66 N ASN B 21 SHEET 3 E 5 VAL B 118 GLU B 125 1 O GLY B 123 N VAL B 67 SHEET 4 E 5 MET B 145 THR B 149 1 O THR B 149 N VAL B 124 SHEET 5 E 5 LEU B 193 ASP B 195 1 O ASP B 195 N LEU B 148 SHEET 1 F 3 ILE B 216 PHE B 217 0 SHEET 2 F 3 LEU B 246 VAL B 249 1 O MET B 248 N PHE B 217 SHEET 3 F 3 VAL B 283 PHE B 285 1 O GLY B 284 N VAL B 249

SSBOND 1 CYS A 71 CYS A 154 1555 1555 2.02 SSBOND 2 CYS A 226 CYS A 258 1555 1555 2.03 SSBOND 3 CYS A 361 CYS B 361 1555 1555 2.03 SSBOND 4 CYS B 71 CYS B 154 1555 1555 2.03 SSBOND 5 CYS B 226 CYS B 258 1555 1555 2.04

LINK ZN ZN A 401 NE2 HIS A 20 1555 1555 2.02 LINK ZN ZN A 401 OD1 ASP A 22 1555 1555 2.05 LINK ZN ZN A 401 OE1 GLU A 125 1555 1555 2.15 LINK ZN ZN A 402 OE2 GLU A 125 1555 1555 2.19 LINK ZN ZN A 402 NE2 HIS A 219 1555 1555 2.09 LINK ZN ZN B 411 NE2 HIS B 20 1555 1555 2.00 LINK ZN ZN B 411 OD1 ASP B 22 1555 1555 2.09 LINK ZN ZN B 411 OE1 GLU B 125 1555 1555 2.14 LINK ZN ZN B 412 OE2 GLU B 125 1555 1555 2.18 LINK ZN ZN B 412 NE2 HIS B 219 1555 1555 2.10 LINK ND2 ASN A 41 C1 NAG A 461 1555 1555 1.45 LINK ND2 ASN A 316 C1 NAG A 463 1555 1555 1.45 LINK ND2 ASN B 41 C1 NAG B 462 1555 1555 1.45 LINK ND2 ASN B 316 C1 NAG B 464 1555 1555 1.45 LINK ZN ZN A 401 O HOH A 421 1555 1555 2.22 LINK ZN ZN A 402 NE2 HIS A 198 1555 1555 2.22 LINK ZN ZN A 402 O13 CIL A 451 1555 1555 2.28 LINK ZN ZN A 402 O HOH A 421 1555 1555 2.12 LINK ZN ZN B 411 O HOH B 422 1555 1555 2.21 LINK ZN ZN B 412 NE2 HIS B 198 1555 1555 2.20 LINK ZN ZN B 412 O HOH B 422 1555 1555 2.19 LINK ZN ZN B 412 O13 CIL B 452 1555 1555 2.42

SITE 1 AC1 5 ASN A 41 THR A 43 MET A 95 HOH A1290 SITE 2 AC1 5 HOH A1343 SITE 1 AC2 4 GLU B 38 ASN B 41 THR B 43 HOH B1515 SITE 1 AC3 2 ASN A 316 HOH B1107 SITE 1 AC4 6 PHE A 2 GLU A 6 ASN B 316 THR B 318 SITE 2 AC4 6 HOH B1489 HOH B1601 SITE 1 AC5 6 HIS A 20 ASP A 22 GLU A 125 ZN A 402 SITE 2 AC5 6 HOH A 421 CIL A 451 SITE 1 AC6 6 GLU A 125 HIS A 198 HIS A 219 ZN A 401 SITE 2 AC6 6 HOH A 421 CIL A 451 SITE 1 AC7 6 HIS B 20 ASP B 22 GLU B 125 ZN B 412 SITE 2 AC7 6 HOH B 422 CIL B 452 SITE 1 AC8 6 GLU B 125 HIS B 198 HIS B 219 ZN B 411 SITE 2 AC8 6 HOH B 422 CIL B 452 SITE 1 AC9 14 ASP A 22 TYR A 68 HIS A 152 HIS A 198 SITE 2 AC9 14 HIS A 219 ARG A 230 TYR A 252 TYR A 255 SITE 3 AC9 14 ASP A 288 GLY A 291 PRO A 293 ZN A 401 SITE 4 AC9 14 ZN A 402 HOH A 421 SITE 1 BC1 13 ASP B 22 TYR B 68 HIS B 152 HIS B 198 SITE 2 BC1 13 HIS B 219 ARG B 230 TYR B 255 ASP B 288 SITE 3 BC1 13 GLY B 291 VAL B 292 ZN B 411 ZN B 412 SITE 4 BC1 13 HOH B 422

CRYST1 80.179 79.491 56.951 90.00 96.34 90.00 P 1 21 1 4

ORIGX1 1.000000 0.000000 0.000000 0.00000

ORIGX2 0.000000 1.000000 0.000000 0.00000

ORIGX3 0.000000 0.000000 1.000000 0.00000

SCALE1 0.012472 0.000000 0.001386 0.00000

SCALE2 0.000000 0.012580 0.000000 0.00000

SCALE3 0.000000 0.000000 0.017667 0.00000