HEADER HYDROLASE 09-NOV-16 5MC2 TITLE CRYSTAL STRUCTURE OF GLY278ASP MUTANT OF HUMAN PROLIDASE WITH MN IONS TITLE 2 AND GLYPRO LIGAND COMPND MOL_ID: 1; COMPND 2 MOLECULE: XAA-PRO DIPEPTIDASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: X-PRO DIPEPTIDASE,IMIDODIPEPTIDASE,PEPTIDASE D,PROLINE COMPND 5 DIPEPTIDASE,PROLIDASE; COMPND 6 EC: 3.4.13.9; 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: PEPD, PRD; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: ROSETTA; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS PROLIDASE, PEPTIDASE, HYDROLYSIS, PITA-BREAD, METALLOENZYME, KEYWDS 2 MUTATION, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR P.WILK,U.MUELLER,H.DOBBEK,M.S.WEISS REVDAT 5 17-JAN-24 5MC2 1 LINK REVDAT 4 22-APR-20 5MC2 1 REMARK REVDAT 3 26-SEP-18 5MC2 1 JRNL REVDAT 2 15-AUG-18 5MC2 1 JRNL REVDAT 1 20-DEC-17 5MC2 0 JRNL AUTH P.WILK,M.UEHLEIN,R.PIWOWARCZYK,H.DOBBEK,U.MUELLER,M.S.WEISS JRNL TITL STRUCTURAL BASIS FOR PROLIDASE DEFICIENCY DISEASE JRNL TITL 2 MECHANISMS. JRNL REF FEBS J. V. 285 3422 2018 JRNL REFN ISSN 1742-4658 JRNL PMID 30066404 JRNL DOI 10.1111/FEBS.14620 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.17 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 130402 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.141 REMARK 3 R VALUE (WORKING SET) : 0.141 REMARK 3 FREE R VALUE : 0.171 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 0.770 REMARK 3 FREE R VALUE TEST SET COUNT : 1005 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 48.1844 - 3.2485 1.00 18968 148 0.1363 0.1506 REMARK 3 2 3.2485 - 2.5785 1.00 18576 144 0.1418 0.1786 REMARK 3 3 2.5785 - 2.2526 1.00 18507 143 0.1236 0.1551 REMARK 3 4 2.2526 - 2.0466 1.00 18477 144 0.1251 0.1655 REMARK 3 5 2.0466 - 1.8999 1.00 18378 142 0.1457 0.1794 REMARK 3 6 1.8999 - 1.7879 1.00 18326 143 0.1862 0.2592 REMARK 3 7 1.7879 - 1.6983 0.99 18165 141 0.2309 0.2876 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.710 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.47 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.12 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.005 8091 REMARK 3 ANGLE : 0.992 11005 REMARK 3 CHIRALITY : 0.038 1195 REMARK 3 PLANARITY : 0.005 1442 REMARK 3 DIHEDRAL : 13.211 3087 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : 1 REMARK 3 NCS GROUP : 1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: CHAIN A REMARK 3 SELECTION : CHAIN B REMARK 3 ATOM PAIRS NUMBER : 5058 REMARK 3 RMSD : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5MC2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-NOV-16. REMARK 100 THE DEPOSITION ID IS D_1200002249. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-JAN-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9184 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR SI REMARK 200 -11 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS, XSCALE REMARK 200 DATA SCALING SOFTWARE : XSCALE, XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 130410 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.698 REMARK 200 RESOLUTION RANGE LOW (A) : 48.165 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 7.510 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.8800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.08300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.850 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.5.6 REMARK 200 STARTING MODEL: 5M4J REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.49 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.76 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10MM NABORATE, 760MM NACITRATE, PH REMARK 280 7.4, VAPOR DIFFUSION, TEMPERATURE 278K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 105.59350 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 105.59350 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 51.92100 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 54.12350 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 51.92100 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 54.12350 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 105.59350 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 51.92100 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 54.12350 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 105.59350 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 51.92100 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 54.12350 REMARK 290 SMTRY3 8 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7440 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 36550 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -42.0 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 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 ALA A 5 REMARK 465 THR A 242 REMARK 465 CYS A 243 REMARK 465 GLY A 257 REMARK 465 HIS A 258 REMARK 465 ALA A 259 REMARK 465 GLY A 260 REMARK 465 PRO A 488 REMARK 465 ALA B 5 REMARK 465 THR B 242 REMARK 465 CYS B 243 REMARK 465 GLU B 249 REMARK 465 ASN B 250 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 C GLY B 503 N PRO B 504 1.34 REMARK 500 C GLY A 503 N PRO A 504 1.34 REMARK 500 OD1 ASP B 287 O HOH B 601 2.10 REMARK 500 O HOH A 627 O HOH A 801 2.11 REMARK 500 OD1 ASP B 276 O HOH B 601 2.12 REMARK 500 OD1 ASP A 287 O HOH A 601 2.15 REMARK 500 OE2 GLU A 131 O HOH A 602 2.15 REMARK 500 OD1 ASP A 276 O HOH A 601 2.16 REMARK 500 O HOH A 604 O HOH A 778 2.19 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 ASN A 13 -121.66 49.05 REMARK 500 TYR A 57 -126.76 48.69 REMARK 500 TYR A 57 -126.76 52.24 REMARK 500 SER A 239 -61.28 -94.59 REMARK 500 ARG A 470 -37.50 -131.44 REMARK 500 ASN B 13 -122.60 48.39 REMARK 500 TYR B 57 -125.86 49.04 REMARK 500 SER B 239 -61.29 -94.71 REMARK 500 TYR B 256 -12.92 -141.57 REMARK 500 ARG B 470 -36.46 -130.14 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 GLY A 503 REMARK 610 GLY B 503 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 NA A 500 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 276 OD2 REMARK 620 2 GLU A 412 OE1 111.2 REMARK 620 3 GLU A 452 OE1 94.4 89.1 REMARK 620 4 GLU A 452 OE2 138.8 74.0 44.4 REMARK 620 5 GLY A 503 O 118.1 97.9 140.8 100.7 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 499 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 287 OD2 REMARK 620 2 HIS A 370 NE2 100.7 REMARK 620 3 GLU A 412 OE2 164.9 79.8 REMARK 620 4 GLU A 452 OE2 85.9 115.1 80.3 REMARK 620 5 GLY A 503 O 96.9 86.2 98.2 157.8 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 500 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 276 OD2 REMARK 620 2 GLU B 412 OE1 110.9 REMARK 620 3 GLU B 452 OE1 97.2 90.3 REMARK 620 4 GLU B 452 OE2 142.2 73.1 45.2 REMARK 620 5 GLY B 503 O 119.0 93.1 139.3 97.7 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 499 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 287 OD2 REMARK 620 2 HIS B 370 NE2 98.1 REMARK 620 3 GLU B 412 OE2 165.9 81.3 REMARK 620 4 GLU B 452 OE2 88.7 117.4 79.2 REMARK 620 5 GLY B 503 O 92.4 86.8 101.6 155.4 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 MN A 499 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GLY A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PRO A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 507 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN B 499 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA B 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GLY B 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PRO B 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 507 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 508 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5M4J RELATED DB: PDB REMARK 900 WILD-TYPE HUMAN PROLIDASE REMARK 900 RELATED ID: 5MBY RELATED DB: PDB REMARK 900 MUTATIONS OF HUMAN PROLIDASE REMARK 900 RELATED ID: 5MBZ RELATED DB: PDB REMARK 900 MUTATIONS OF HUMAN PROLIDASE REMARK 900 RELATED ID: 5MC0 RELATED DB: PDB REMARK 900 MUTATIONS OF HUMAN PROLIDASE REMARK 900 RELATED ID: 5MC1 RELATED DB: PDB REMARK 900 MUTATIONS OF HUMAN PROLIDASE REMARK 900 RELATED ID: 5MC3 RELATED DB: PDB REMARK 900 MUTATIONS OF HUMAN PROLIDASE REMARK 900 RELATED ID: 5MC4 RELATED DB: PDB REMARK 900 MUTATIONS OF HUMAN PROLIDASE REMARK 900 RELATED ID: 5MC5 RELATED DB: PDB REMARK 900 MUTATIONS OF HUMAN PROLIDASE DBREF 5MC2 A 6 488 UNP P12955 PEPD_HUMAN 6 488 DBREF 5MC2 B 6 488 UNP P12955 PEPD_HUMAN 6 488 SEQADV 5MC2 ALA A 5 UNP P12955 EXPRESSION TAG SEQADV 5MC2 ASP A 278 UNP P12955 GLY 278 ENGINEERED MUTATION SEQADV 5MC2 ALA B 5 UNP P12955 EXPRESSION TAG SEQADV 5MC2 ASP B 278 UNP P12955 GLY 278 ENGINEERED MUTATION SEQRES 1 A 484 ALA GLY PRO SER PHE TRP LEU GLY ASN GLU THR LEU LYS SEQRES 2 A 484 VAL PRO LEU ALA LEU PHE ALA LEU ASN ARG GLN ARG LEU SEQRES 3 A 484 CYS GLU ARG LEU ARG LYS ASN PRO ALA VAL GLN ALA GLY SEQRES 4 A 484 SER ILE VAL VAL LEU GLN GLY GLY GLU GLU THR GLN ARG SEQRES 5 A 484 TYR CYS THR ASP THR GLY VAL LEU PHE ARG GLN GLU SER SEQRES 6 A 484 PHE PHE HIS TRP ALA PHE GLY VAL THR GLU PRO GLY CYS SEQRES 7 A 484 TYR GLY VAL ILE ASP VAL ASP THR GLY LYS SER THR LEU SEQRES 8 A 484 PHE VAL PRO ARG LEU PRO ALA SER HIS ALA THR TRP MET SEQRES 9 A 484 GLY LYS ILE HIS SER LYS GLU HIS PHE LYS GLU LYS TYR SEQRES 10 A 484 ALA VAL ASP ASP VAL GLN TYR VAL ASP GLU ILE ALA SER SEQRES 11 A 484 VAL LEU THR SER GLN LYS PRO SER VAL LEU LEU THR LEU SEQRES 12 A 484 ARG GLY VAL ASN THR ASP SER GLY SER VAL CYS ARG GLU SEQRES 13 A 484 ALA SER PHE ASP GLY ILE SER LYS PHE GLU VAL ASN ASN SEQRES 14 A 484 THR ILE LEU HIS PRO GLU ILE VAL GLU CYS ARG VAL PHE SEQRES 15 A 484 LYS THR ASP MET GLU LEU GLU VAL LEU ARG TYR THR ASN SEQRES 16 A 484 LYS ILE SER SER GLU ALA HIS ARG GLU VAL MET LYS ALA SEQRES 17 A 484 VAL LYS VAL GLY MET LYS GLU TYR GLU LEU GLU SER LEU SEQRES 18 A 484 PHE GLU HIS TYR CYS TYR SER ARG GLY GLY MET ARG HIS SEQRES 19 A 484 SER SER TYR THR CYS ILE CYS GLY SER GLY GLU ASN SER SEQRES 20 A 484 ALA VAL LEU HIS TYR GLY HIS ALA GLY ALA PRO ASN ASP SEQRES 21 A 484 ARG THR ILE GLN ASN GLY ASP MET CYS LEU PHE ASP MET SEQRES 22 A 484 ASP GLY GLU TYR TYR CYS PHE ALA SER ASP ILE THR CYS SEQRES 23 A 484 SER PHE PRO ALA ASN GLY LYS PHE THR ALA ASP GLN LYS SEQRES 24 A 484 ALA VAL TYR GLU ALA VAL LEU ARG SER SER ARG ALA VAL SEQRES 25 A 484 MET GLY ALA MET LYS PRO GLY VAL TRP TRP PRO ASP MET SEQRES 26 A 484 HIS ARG LEU ALA ASP ARG ILE HIS LEU GLU GLU LEU ALA SEQRES 27 A 484 HIS MET GLY ILE LEU SER GLY SER VAL ASP ALA MET VAL SEQRES 28 A 484 GLN ALA HIS LEU GLY ALA VAL PHE MET PRO HIS GLY LEU SEQRES 29 A 484 GLY HIS PHE LEU GLY ILE ASP VAL HIS ASP VAL GLY GLY SEQRES 30 A 484 TYR PRO GLU GLY VAL GLU ARG ILE ASP GLU PRO GLY LEU SEQRES 31 A 484 ARG SER LEU ARG THR ALA ARG HIS LEU GLN PRO GLY MET SEQRES 32 A 484 VAL LEU THR VAL GLU PRO GLY ILE TYR PHE ILE ASP HIS SEQRES 33 A 484 LEU LEU ASP GLU ALA LEU ALA ASP PRO ALA ARG ALA SER SEQRES 34 A 484 PHE LEU ASN ARG GLU VAL LEU GLN ARG PHE ARG GLY PHE SEQRES 35 A 484 GLY GLY VAL ARG ILE GLU GLU ASP VAL VAL VAL THR ASP SEQRES 36 A 484 SER GLY ILE GLU LEU LEU THR CYS VAL PRO ARG THR VAL SEQRES 37 A 484 GLU GLU ILE GLU ALA CYS MET ALA GLY CYS ASP LYS ALA SEQRES 38 A 484 PHE THR PRO SEQRES 1 B 484 ALA GLY PRO SER PHE TRP LEU GLY ASN GLU THR LEU LYS SEQRES 2 B 484 VAL PRO LEU ALA LEU PHE ALA LEU ASN ARG GLN ARG LEU SEQRES 3 B 484 CYS GLU ARG LEU ARG LYS ASN PRO ALA VAL GLN ALA GLY SEQRES 4 B 484 SER ILE VAL VAL LEU GLN GLY GLY GLU GLU THR GLN ARG SEQRES 5 B 484 TYR CYS THR ASP THR GLY VAL LEU PHE ARG GLN GLU SER SEQRES 6 B 484 PHE PHE HIS TRP ALA PHE GLY VAL THR GLU PRO GLY CYS SEQRES 7 B 484 TYR GLY VAL ILE ASP VAL ASP THR GLY LYS SER THR LEU SEQRES 8 B 484 PHE VAL PRO ARG LEU PRO ALA SER HIS ALA THR TRP MET SEQRES 9 B 484 GLY LYS ILE HIS SER LYS GLU HIS PHE LYS GLU LYS TYR SEQRES 10 B 484 ALA VAL ASP ASP VAL GLN TYR VAL ASP GLU ILE ALA SER SEQRES 11 B 484 VAL LEU THR SER GLN LYS PRO SER VAL LEU LEU THR LEU SEQRES 12 B 484 ARG GLY VAL ASN THR ASP SER GLY SER VAL CYS ARG GLU SEQRES 13 B 484 ALA SER PHE ASP GLY ILE SER LYS PHE GLU VAL ASN ASN SEQRES 14 B 484 THR ILE LEU HIS PRO GLU ILE VAL GLU CYS ARG VAL PHE SEQRES 15 B 484 LYS THR ASP MET GLU LEU GLU VAL LEU ARG TYR THR ASN SEQRES 16 B 484 LYS ILE SER SER GLU ALA HIS ARG GLU VAL MET LYS ALA SEQRES 17 B 484 VAL LYS VAL GLY MET LYS GLU TYR GLU LEU GLU SER LEU SEQRES 18 B 484 PHE GLU HIS TYR CYS TYR SER ARG GLY GLY MET ARG HIS SEQRES 19 B 484 SER SER TYR THR CYS ILE CYS GLY SER GLY GLU ASN SER SEQRES 20 B 484 ALA VAL LEU HIS TYR GLY HIS ALA GLY ALA PRO ASN ASP SEQRES 21 B 484 ARG THR ILE GLN ASN GLY ASP MET CYS LEU PHE ASP MET SEQRES 22 B 484 ASP GLY GLU TYR TYR CYS PHE ALA SER ASP ILE THR CYS SEQRES 23 B 484 SER PHE PRO ALA ASN GLY LYS PHE THR ALA ASP GLN LYS SEQRES 24 B 484 ALA VAL TYR GLU ALA VAL LEU ARG SER SER ARG ALA VAL SEQRES 25 B 484 MET GLY ALA MET LYS PRO GLY VAL TRP TRP PRO ASP MET SEQRES 26 B 484 HIS ARG LEU ALA ASP ARG ILE HIS LEU GLU GLU LEU ALA SEQRES 27 B 484 HIS MET GLY ILE LEU SER GLY SER VAL ASP ALA MET VAL SEQRES 28 B 484 GLN ALA HIS LEU GLY ALA VAL PHE MET PRO HIS GLY LEU SEQRES 29 B 484 GLY HIS PHE LEU GLY ILE ASP VAL HIS ASP VAL GLY GLY SEQRES 30 B 484 TYR PRO GLU GLY VAL GLU ARG ILE ASP GLU PRO GLY LEU SEQRES 31 B 484 ARG SER LEU ARG THR ALA ARG HIS LEU GLN PRO GLY MET SEQRES 32 B 484 VAL LEU THR VAL GLU PRO GLY ILE TYR PHE ILE ASP HIS SEQRES 33 B 484 LEU LEU ASP GLU ALA LEU ALA ASP PRO ALA ARG ALA SER SEQRES 34 B 484 PHE LEU ASN ARG GLU VAL LEU GLN ARG PHE ARG GLY PHE SEQRES 35 B 484 GLY GLY VAL ARG ILE GLU GLU ASP VAL VAL VAL THR ASP SEQRES 36 B 484 SER GLY ILE GLU LEU LEU THR CYS VAL PRO ARG THR VAL SEQRES 37 B 484 GLU GLU ILE GLU ALA CYS MET ALA GLY CYS ASP LYS ALA SEQRES 38 B 484 PHE THR PRO HET MN A 499 1 HET NA A 500 1 HET GLY A 503 4 HET PRO A 504 8 HET GOL A 505 6 HET GOL A 506 6 HET GOL A 507 6 HET MN B 499 1 HET NA B 500 1 HET GLY B 503 4 HET PRO B 504 8 HET GOL B 505 6 HET GOL B 506 6 HET GOL B 507 6 HET GOL B 508 6 HETNAM MN MANGANESE (II) ION HETNAM NA SODIUM ION HETNAM GLY GLYCINE HETNAM PRO PROLINE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 MN 2(MN 2+) FORMUL 4 NA 2(NA 1+) FORMUL 5 GLY 2(C2 H5 N O2) FORMUL 6 PRO 2(C5 H9 N O2) FORMUL 7 GOL 7(C3 H8 O3) FORMUL 18 HOH *877(H2 O) HELIX 1 AA1 LEU A 20 ASN A 37 1 18 HELIX 2 AA2 GLU A 68 GLY A 76 1 9 HELIX 3 AA3 ALA A 102 MET A 108 1 7 HELIX 4 AA4 SER A 113 ALA A 122 1 10 HELIX 5 AA5 GLU A 131 GLN A 139 1 9 HELIX 6 AA6 GLY A 165 PHE A 169 5 5 HELIX 7 AA7 ILE A 175 PHE A 186 1 12 HELIX 8 AA8 THR A 188 VAL A 213 1 26 HELIX 9 AA9 LYS A 218 GLY A 235 1 18 HELIX 10 AB1 GLU A 249 ALA A 252 5 4 HELIX 11 AB2 THR A 299 MET A 320 1 22 HELIX 12 AB3 TRP A 325 MET A 344 1 20 HELIX 13 AB4 SER A 350 ALA A 357 1 8 HELIX 14 AB5 LEU A 359 MET A 364 1 6 HELIX 15 AB6 GLY A 393 LEU A 397 5 5 HELIX 16 AB7 ILE A 418 ASP A 428 1 11 HELIX 17 AB8 ASP A 428 SER A 433 1 6 HELIX 18 AB9 ASN A 436 GLN A 441 1 6 HELIX 19 AC1 ARG A 442 ARG A 444 5 3 HELIX 20 AC2 THR A 471 ALA A 480 1 10 HELIX 21 AC3 LEU B 20 LYS B 36 1 17 HELIX 22 AC4 GLU B 68 GLY B 76 1 9 HELIX 23 AC5 SER B 103 MET B 108 1 6 HELIX 24 AC6 SER B 113 ALA B 122 1 10 HELIX 25 AC7 GLU B 131 LYS B 140 1 10 HELIX 26 AC8 GLY B 165 PHE B 169 5 5 HELIX 27 AC9 ILE B 175 PHE B 186 1 12 HELIX 28 AD1 THR B 188 VAL B 213 1 26 HELIX 29 AD2 LYS B 218 GLY B 235 1 18 HELIX 30 AD3 ALA B 252 GLY B 257 1 6 HELIX 31 AD4 THR B 299 MET B 320 1 22 HELIX 32 AD5 TRP B 325 MET B 344 1 20 HELIX 33 AD6 SER B 350 ALA B 357 1 8 HELIX 34 AD7 LEU B 359 MET B 364 1 6 HELIX 35 AD8 GLY B 393 LEU B 397 5 5 HELIX 36 AD9 ILE B 418 ASP B 428 1 11 HELIX 37 AE1 ASP B 428 SER B 433 1 6 HELIX 38 AE2 ASN B 436 GLN B 441 1 6 HELIX 39 AE3 ARG B 442 ARG B 444 5 3 HELIX 40 AE4 THR B 471 ALA B 480 1 10 SHEET 1 AA1 2 SER A 8 PHE A 9 0 SHEET 2 AA1 2 VAL A 18 PRO A 19 -1 O VAL A 18 N PHE A 9 SHEET 1 AA2 6 ASP A 125 TYR A 128 0 SHEET 2 AA2 6 SER A 93 VAL A 97 1 N VAL A 97 O GLN A 127 SHEET 3 AA2 6 TYR A 83 ASP A 87 -1 N TYR A 83 O PHE A 96 SHEET 4 AA2 6 ILE A 45 GLN A 49 -1 N LEU A 48 O GLY A 84 SHEET 5 AA2 6 LEU A 144 LEU A 145 1 O LEU A 145 N ILE A 45 SHEET 6 AA2 6 VAL A 171 ASN A 172 1 O ASN A 172 N LEU A 144 SHEET 1 AA3 3 CYS A 245 SER A 247 0 SHEET 2 AA3 3 MET A 272 TYR A 281 -1 O LEU A 274 N GLY A 246 SHEET 3 AA3 3 PHE A 284 PRO A 293 -1 O CYS A 290 N PHE A 275 SHEET 1 AA4 3 VAL A 408 VAL A 411 0 SHEET 2 AA4 3 GLU A 453 VAL A 457 -1 O VAL A 455 N LEU A 409 SHEET 3 AA4 3 ILE A 462 LEU A 464 -1 O GLU A 463 N VAL A 456 SHEET 1 AA5 2 GLY A 414 TYR A 416 0 SHEET 2 AA5 2 GLY A 448 ARG A 450 -1 O VAL A 449 N ILE A 415 SHEET 1 AA6 2 SER B 8 PHE B 9 0 SHEET 2 AA6 2 VAL B 18 PRO B 19 -1 O VAL B 18 N PHE B 9 SHEET 1 AA7 6 ASP B 125 TYR B 128 0 SHEET 2 AA7 6 SER B 93 VAL B 97 1 N LEU B 95 O ASP B 125 SHEET 3 AA7 6 TYR B 83 ASP B 87 -1 N TYR B 83 O PHE B 96 SHEET 4 AA7 6 ILE B 45 GLN B 49 -1 N VAL B 46 O ILE B 86 SHEET 5 AA7 6 LEU B 144 LEU B 145 1 O LEU B 145 N ILE B 45 SHEET 6 AA7 6 VAL B 171 ASN B 172 1 O ASN B 172 N LEU B 144 SHEET 1 AA8 3 ARG B 237 HIS B 238 0 SHEET 2 AA8 3 MET B 272 TYR B 281 -1 O GLU B 280 N ARG B 237 SHEET 3 AA8 3 CYS B 245 SER B 247 -1 N GLY B 246 O LEU B 274 SHEET 1 AA9 3 ARG B 237 HIS B 238 0 SHEET 2 AA9 3 MET B 272 TYR B 281 -1 O GLU B 280 N ARG B 237 SHEET 3 AA9 3 PHE B 284 PRO B 293 -1 O PHE B 292 N CYS B 273 SHEET 1 AB1 3 VAL B 408 VAL B 411 0 SHEET 2 AB1 3 GLU B 453 VAL B 457 -1 O VAL B 455 N LEU B 409 SHEET 3 AB1 3 ILE B 462 LEU B 464 -1 O GLU B 463 N VAL B 456 SHEET 1 AB2 2 GLY B 414 TYR B 416 0 SHEET 2 AB2 2 GLY B 448 ARG B 450 -1 O VAL B 449 N ILE B 415 SSBOND 1 CYS A 482 CYS A 482 1555 3555 2.04 SSBOND 2 CYS B 482 CYS B 482 1555 3555 2.02 LINK OD2 ASP A 276 NA NA A 500 1555 1555 2.86 LINK OD2 ASP A 287 MN MN A 499 1555 1555 2.10 LINK NE2 HIS A 370 MN MN A 499 1555 1555 2.37 LINK OE2 GLU A 412 MN MN A 499 1555 1555 2.36 LINK OE1 GLU A 412 NA NA A 500 1555 1555 2.59 LINK OE2 GLU A 452 MN MN A 499 1555 1555 2.30 LINK OE1 GLU A 452 NA NA A 500 1555 1555 2.81 LINK OE2 GLU A 452 NA NA A 500 1555 1555 3.03 LINK MN MN A 499 O GLY A 503 1555 1555 2.48 LINK NA NA A 500 O GLY A 503 1555 1555 3.06 LINK OD2 ASP B 276 NA NA B 500 1555 1555 2.72 LINK OD2 ASP B 287 MN MN B 499 1555 1555 2.22 LINK NE2 HIS B 370 MN MN B 499 1555 1555 2.36 LINK OE2 GLU B 412 MN MN B 499 1555 1555 2.34 LINK OE1 GLU B 412 NA NA B 500 1555 1555 2.67 LINK OE2 GLU B 452 MN MN B 499 1555 1555 2.27 LINK OE1 GLU B 452 NA NA B 500 1555 1555 2.69 LINK OE2 GLU B 452 NA NA B 500 1555 1555 2.98 LINK MN MN B 499 O GLY B 503 1555 1555 2.47 LINK NA NA B 500 O GLY B 503 1555 1555 3.17 SITE 1 AC1 6 ASP A 287 HIS A 370 GLU A 412 GLU A 452 SITE 2 AC1 6 NA A 500 GLY A 503 SITE 1 AC2 7 ASP A 276 ASP A 287 GLU A 412 GLU A 452 SITE 2 AC2 7 MN A 499 GLY A 503 PRO A 504 SITE 1 AC3 10 ASP A 276 ASP A 287 HIS A 370 HIS A 377 SITE 2 AC3 10 GLU A 412 MN A 499 NA A 500 PRO A 504 SITE 3 AC3 10 HOH A 707 HOH A 823 SITE 1 AC4 10 HIS A 255 HIS A 366 HIS A 377 ARG A 398 SITE 2 AC4 10 GLU A 412 ARG A 450 NA A 500 GLY A 503 SITE 3 AC4 10 HOH A 683 HOH A 867 SITE 1 AC5 5 GLN A 28 ARG A 35 THR A 90 HOH A 605 SITE 2 AC5 5 HOH A 793 SITE 1 AC6 4 HOH A 767 LYS B 297 PHE B 298 HOH B 867 SITE 1 AC7 3 THR A 152 GLU A 387 ARG A 388 SITE 1 AC8 6 ASP B 287 HIS B 370 GLU B 412 GLU B 452 SITE 2 AC8 6 NA B 500 GLY B 503 SITE 1 AC9 7 ASP B 276 ASP B 287 GLU B 412 GLU B 452 SITE 2 AC9 7 MN B 499 GLY B 503 PRO B 504 SITE 1 AD1 9 ASP B 276 ASP B 287 HIS B 370 HIS B 377 SITE 2 AD1 9 MN B 499 NA B 500 PRO B 504 HOH B 812 SITE 3 AD1 9 HOH B 850 SITE 1 AD2 9 HIS B 366 HIS B 377 ARG B 398 GLU B 412 SITE 2 AD2 9 ARG B 450 NA B 500 GLY B 503 HOH B 727 SITE 3 AD2 9 HOH B 758 SITE 1 AD3 3 SER B 433 LEU B 435 ASN B 436 SITE 1 AD4 4 TRP B 325 HIS B 402 HOH B 627 HOH B 655 SITE 1 AD5 5 ARG B 29 ARG B 33 CYS B 183 PHE B 186 SITE 2 AD5 5 HOH B 697 SITE 1 AD6 3 HIS B 402 HOH B 606 HOH B 705 CRYST1 103.842 108.247 211.187 90.00 90.00 90.00 C 2 2 21 16 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 0.009630 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009238 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004735 0.00000