HEADER HYDROLASE 20-FEB-19 6QSB TITLE CRYSTAL STRUCTURE OF ARG470HIS MUTANT OF HUMAN PROLIDASE WITH MN IONS 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(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS HYDROLASE, METAL BINDING, DIPEPTIDASE, MUTATION EXPDTA X-RAY DIFFRACTION AUTHOR P.WILK,E.WATOR,M.S.WEISS REVDAT 3 06-MAR-24 6QSB 1 JRNL REVDAT 2 24-JAN-24 6QSB 1 LINK REVDAT 1 18-MAR-20 6QSB 0 JRNL AUTH N.D.LINHARES,P.WILK,E.WATOR,M.A.TOSTES,M.S.WEISS,S.D.J.PENA JRNL TITL STRUCTURAL ANALYSIS OF NEW COMPOUND HETEROZYGOUS VARIANTS IN JRNL TITL 2 PEPD GENE IDENTIFIED IN A PATIENT WITH PROLIDASE DEFICIENCY JRNL TITL 3 DIAGNOSED BY EXOME SEQUENCING. JRNL REF GENET MOL BIOL V. 44 00393 2021 JRNL REFN ISSN 1415-4757 JRNL PMID 33877262 JRNL DOI 10.1590/1678-4685-GMB-2020-0393 REMARK 2 REMARK 2 RESOLUTION. 1.99 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.99 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.37 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 81666 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.189 REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.570 REMARK 3 FREE R VALUE TEST SET COUNT : 2097 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 23.3676 - 4.8906 0.99 5503 145 0.1742 0.1872 REMARK 3 2 4.8906 - 3.8876 1.00 5396 143 0.1213 0.1349 REMARK 3 3 3.8876 - 3.3979 1.00 5356 141 0.1363 0.1828 REMARK 3 4 3.3979 - 3.0880 1.00 5345 140 0.1634 0.2122 REMARK 3 5 3.0880 - 2.8671 1.00 5320 141 0.1812 0.2054 REMARK 3 6 2.8671 - 2.6983 1.00 5300 139 0.2011 0.2474 REMARK 3 7 2.6983 - 2.5633 1.00 5296 140 0.2180 0.2780 REMARK 3 8 2.5633 - 2.4519 1.00 5297 139 0.2316 0.2890 REMARK 3 9 2.4519 - 2.3576 1.00 5253 139 0.2374 0.2881 REMARK 3 10 2.3576 - 2.2763 1.00 5288 139 0.2588 0.2943 REMARK 3 11 2.2763 - 2.2052 1.00 5262 139 0.2712 0.3178 REMARK 3 12 2.2052 - 2.1422 1.00 5283 139 0.2890 0.3514 REMARK 3 13 2.1422 - 2.0858 1.00 5249 138 0.3046 0.3306 REMARK 3 14 2.0858 - 2.0350 1.00 5284 140 0.3235 0.3539 REMARK 3 15 2.0350 - 1.9887 0.98 5137 135 0.3618 0.4146 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.320 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.580 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 34.08 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 43.07 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6QSB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 20-FEB-19. REMARK 100 THE DEPOSITION ID IS D_1292100785. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-DEC-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9180 REMARK 200 MONOCHROMATOR : KMC-1 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 81795 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.990 REMARK 200 RESOLUTION RANGE LOW (A) : 48.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 6.870 REMARK 200 R MERGE (I) : 0.34000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.4300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.99 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.01 REMARK 200 R MERGE FOR SHELL (I) : 2.84200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.630 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.8.1 REMARK 200 STARTING MODEL: 5M4Q REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.77 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10MM NATETRABORATE, 690-760MM REMARK 280 NACITRATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 105.90200 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 105.90200 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 51.77750 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 54.26650 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 51.77750 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 54.26650 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 105.90200 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 51.77750 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 54.26650 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 105.90200 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 51.77750 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 54.26650 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: 8060 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 35260 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -58.0 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 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 813 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 ALA A 3 REMARK 465 ALA A 4 REMARK 465 THR A 5 REMARK 465 ALA A 485 REMARK 465 PHE A 486 REMARK 465 THR A 487 REMARK 465 PRO A 488 REMARK 465 PHE A 489 REMARK 465 SER A 490 REMARK 465 GLY A 491 REMARK 465 PRO A 492 REMARK 465 LYS A 493 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 ALA B 3 REMARK 465 ALA B 4 REMARK 465 THR B 5 REMARK 465 PHE B 489 REMARK 465 SER B 490 REMARK 465 GLY B 491 REMARK 465 PRO B 492 REMARK 465 LYS B 493 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 OE2 GLU B 307 O HOH B 601 1.47 REMARK 500 CE LYS A 110 NE2 HIS A 112 1.95 REMARK 500 O MET A 479 O2 GOL A 503 1.99 REMARK 500 O LYS A 211 O1 GOL A 503 2.04 REMARK 500 O HOH A 607 O HOH A 792 2.15 REMARK 500 O HOH B 911 O HOH B 918 2.16 REMARK 500 O1 GOL A 505 O HOH A 601 2.16 REMARK 500 REMARK 500 REMARK: NULL 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 GLU B 307 N GLU B 307 CA 0.121 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 -125.48 49.67 REMARK 500 TYR A 57 -120.36 47.07 REMARK 500 CYS A 245 73.02 -117.21 REMARK 500 ASN B 13 -124.19 49.08 REMARK 500 TYR B 57 -121.25 48.08 REMARK 500 CYS B 245 72.11 -118.60 REMARK 500 HIS B 255 61.79 -103.21 REMARK 500 THR B 458 -169.02 -101.85 REMARK 500 REMARK 500 REMARK: NULL 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 MN A 500 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 276 OD1 REMARK 620 2 ASP A 276 OD2 57.6 REMARK 620 3 ASP A 287 OD1 89.9 147.0 REMARK 620 4 GLU A 452 OE1 102.5 106.7 84.1 REMARK 620 5 HOH A 915 O 101.5 96.6 83.7 153.0 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 89.5 REMARK 620 3 GLU A 412 OE2 156.5 88.5 REMARK 620 4 GLU A 452 OE2 78.0 123.7 83.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 500 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 276 OD1 REMARK 620 2 ASP B 276 OD2 61.0 REMARK 620 3 ASP B 287 OD1 89.6 149.8 REMARK 620 4 GLU B 452 OE1 100.8 98.8 93.4 REMARK 620 5 HOH B 910 O 100.6 91.9 86.3 158.6 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 89.4 REMARK 620 3 GLU B 412 OE2 158.2 85.4 REMARK 620 4 GLU B 452 OE2 81.6 128.2 85.0 REMARK 620 N 1 2 3 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 MN A 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL 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 MN B 499 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN B 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 506 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5M4G RELATED DB: PDB REMARK 900 NATIVE STRUCTURE REMARK 900 RELATED ID: 5M4J RELATED DB: PDB REMARK 900 NATIVE STRUCTURE REMARK 900 RELATED ID: 5MBZ RELATED DB: PDB REMARK 900 RELATED MUTANT DBREF 6QSB A 1 493 UNP P12955 PEPD_HUMAN 1 493 DBREF 6QSB B 1 493 UNP P12955 PEPD_HUMAN 1 493 SEQADV 6QSB HIS A 470 UNP P12955 ARG 470 ENGINEERED MUTATION SEQADV 6QSB HIS B 470 UNP P12955 ARG 470 ENGINEERED MUTATION SEQRES 1 A 493 MET ALA ALA ALA THR GLY PRO SER PHE TRP LEU GLY ASN SEQRES 2 A 493 GLU THR LEU LYS VAL PRO LEU ALA LEU PHE ALA LEU ASN SEQRES 3 A 493 ARG GLN ARG LEU CYS GLU ARG LEU ARG LYS ASN PRO ALA SEQRES 4 A 493 VAL GLN ALA GLY SER ILE VAL VAL LEU GLN GLY GLY GLU SEQRES 5 A 493 GLU THR GLN ARG TYR CYS THR ASP THR GLY VAL LEU PHE SEQRES 6 A 493 ARG GLN GLU SER PHE PHE HIS TRP ALA PHE GLY VAL THR SEQRES 7 A 493 GLU PRO GLY CYS TYR GLY VAL ILE ASP VAL ASP THR GLY SEQRES 8 A 493 LYS SER THR LEU PHE VAL PRO ARG LEU PRO ALA SER HIS SEQRES 9 A 493 ALA THR TRP MET GLY LYS ILE HIS SER LYS GLU HIS PHE SEQRES 10 A 493 LYS GLU LYS TYR ALA VAL ASP ASP VAL GLN TYR VAL ASP SEQRES 11 A 493 GLU ILE ALA SER VAL LEU THR SER GLN LYS PRO SER VAL SEQRES 12 A 493 LEU LEU THR LEU ARG GLY VAL ASN THR ASP SER GLY SER SEQRES 13 A 493 VAL CYS ARG GLU ALA SER PHE ASP GLY ILE SER LYS PHE SEQRES 14 A 493 GLU VAL ASN ASN THR ILE LEU HIS PRO GLU ILE VAL GLU SEQRES 15 A 493 CYS ARG VAL PHE LYS THR ASP MET GLU LEU GLU VAL LEU SEQRES 16 A 493 ARG TYR THR ASN LYS ILE SER SER GLU ALA HIS ARG GLU SEQRES 17 A 493 VAL MET LYS ALA VAL LYS VAL GLY MET LYS GLU TYR GLU SEQRES 18 A 493 LEU GLU SER LEU PHE GLU HIS TYR CYS TYR SER ARG GLY SEQRES 19 A 493 GLY MET ARG HIS SER SER TYR THR CYS ILE CYS GLY SER SEQRES 20 A 493 GLY GLU ASN SER ALA VAL LEU HIS TYR GLY HIS ALA GLY SEQRES 21 A 493 ALA PRO ASN ASP ARG THR ILE GLN ASN GLY ASP MET CYS SEQRES 22 A 493 LEU PHE ASP MET GLY GLY GLU TYR TYR CYS PHE ALA SER SEQRES 23 A 493 ASP ILE THR CYS SER PHE PRO ALA ASN GLY LYS PHE THR SEQRES 24 A 493 ALA ASP GLN LYS ALA VAL TYR GLU ALA VAL LEU ARG SER SEQRES 25 A 493 SER ARG ALA VAL MET GLY ALA MET LYS PRO GLY VAL TRP SEQRES 26 A 493 TRP PRO ASP MET HIS ARG LEU ALA ASP ARG ILE HIS LEU SEQRES 27 A 493 GLU GLU LEU ALA HIS MET GLY ILE LEU SER GLY SER VAL SEQRES 28 A 493 ASP ALA MET VAL GLN ALA HIS LEU GLY ALA VAL PHE MET SEQRES 29 A 493 PRO HIS GLY LEU GLY HIS PHE LEU GLY ILE ASP VAL HIS SEQRES 30 A 493 ASP VAL GLY GLY TYR PRO GLU GLY VAL GLU ARG ILE ASP SEQRES 31 A 493 GLU PRO GLY LEU ARG SER LEU ARG THR ALA ARG HIS LEU SEQRES 32 A 493 GLN PRO GLY MET VAL LEU THR VAL GLU PRO GLY ILE TYR SEQRES 33 A 493 PHE ILE ASP HIS LEU LEU ASP GLU ALA LEU ALA ASP PRO SEQRES 34 A 493 ALA ARG ALA SER PHE LEU ASN ARG GLU VAL LEU GLN ARG SEQRES 35 A 493 PHE ARG GLY PHE GLY GLY VAL ARG ILE GLU GLU ASP VAL SEQRES 36 A 493 VAL VAL THR ASP SER GLY ILE GLU LEU LEU THR CYS VAL SEQRES 37 A 493 PRO HIS THR VAL GLU GLU ILE GLU ALA CYS MET ALA GLY SEQRES 38 A 493 CYS ASP LYS ALA PHE THR PRO PHE SER GLY PRO LYS SEQRES 1 B 493 MET ALA ALA ALA THR GLY PRO SER PHE TRP LEU GLY ASN SEQRES 2 B 493 GLU THR LEU LYS VAL PRO LEU ALA LEU PHE ALA LEU ASN SEQRES 3 B 493 ARG GLN ARG LEU CYS GLU ARG LEU ARG LYS ASN PRO ALA SEQRES 4 B 493 VAL GLN ALA GLY SER ILE VAL VAL LEU GLN GLY GLY GLU SEQRES 5 B 493 GLU THR GLN ARG TYR CYS THR ASP THR GLY VAL LEU PHE SEQRES 6 B 493 ARG GLN GLU SER PHE PHE HIS TRP ALA PHE GLY VAL THR SEQRES 7 B 493 GLU PRO GLY CYS TYR GLY VAL ILE ASP VAL ASP THR GLY SEQRES 8 B 493 LYS SER THR LEU PHE VAL PRO ARG LEU PRO ALA SER HIS SEQRES 9 B 493 ALA THR TRP MET GLY LYS ILE HIS SER LYS GLU HIS PHE SEQRES 10 B 493 LYS GLU LYS TYR ALA VAL ASP ASP VAL GLN TYR VAL ASP SEQRES 11 B 493 GLU ILE ALA SER VAL LEU THR SER GLN LYS PRO SER VAL SEQRES 12 B 493 LEU LEU THR LEU ARG GLY VAL ASN THR ASP SER GLY SER SEQRES 13 B 493 VAL CYS ARG GLU ALA SER PHE ASP GLY ILE SER LYS PHE SEQRES 14 B 493 GLU VAL ASN ASN THR ILE LEU HIS PRO GLU ILE VAL GLU SEQRES 15 B 493 CYS ARG VAL PHE LYS THR ASP MET GLU LEU GLU VAL LEU SEQRES 16 B 493 ARG TYR THR ASN LYS ILE SER SER GLU ALA HIS ARG GLU SEQRES 17 B 493 VAL MET LYS ALA VAL LYS VAL GLY MET LYS GLU TYR GLU SEQRES 18 B 493 LEU GLU SER LEU PHE GLU HIS TYR CYS TYR SER ARG GLY SEQRES 19 B 493 GLY MET ARG HIS SER SER TYR THR CYS ILE CYS GLY SER SEQRES 20 B 493 GLY GLU ASN SER ALA VAL LEU HIS TYR GLY HIS ALA GLY SEQRES 21 B 493 ALA PRO ASN ASP ARG THR ILE GLN ASN GLY ASP MET CYS SEQRES 22 B 493 LEU PHE ASP MET GLY GLY GLU TYR TYR CYS PHE ALA SER SEQRES 23 B 493 ASP ILE THR CYS SER PHE PRO ALA ASN GLY LYS PHE THR SEQRES 24 B 493 ALA ASP GLN LYS ALA VAL TYR GLU ALA VAL LEU ARG SER SEQRES 25 B 493 SER ARG ALA VAL MET GLY ALA MET LYS PRO GLY VAL TRP SEQRES 26 B 493 TRP PRO ASP MET HIS ARG LEU ALA ASP ARG ILE HIS LEU SEQRES 27 B 493 GLU GLU LEU ALA HIS MET GLY ILE LEU SER GLY SER VAL SEQRES 28 B 493 ASP ALA MET VAL GLN ALA HIS LEU GLY ALA VAL PHE MET SEQRES 29 B 493 PRO HIS GLY LEU GLY HIS PHE LEU GLY ILE ASP VAL HIS SEQRES 30 B 493 ASP VAL GLY GLY TYR PRO GLU GLY VAL GLU ARG ILE ASP SEQRES 31 B 493 GLU PRO GLY LEU ARG SER LEU ARG THR ALA ARG HIS LEU SEQRES 32 B 493 GLN PRO GLY MET VAL LEU THR VAL GLU PRO GLY ILE TYR SEQRES 33 B 493 PHE ILE ASP HIS LEU LEU ASP GLU ALA LEU ALA ASP PRO SEQRES 34 B 493 ALA ARG ALA SER PHE LEU ASN ARG GLU VAL LEU GLN ARG SEQRES 35 B 493 PHE ARG GLY PHE GLY GLY VAL ARG ILE GLU GLU ASP VAL SEQRES 36 B 493 VAL VAL THR ASP SER GLY ILE GLU LEU LEU THR CYS VAL SEQRES 37 B 493 PRO HIS THR VAL GLU GLU ILE GLU ALA CYS MET ALA GLY SEQRES 38 B 493 CYS ASP LYS ALA PHE THR PRO PHE SER GLY PRO LYS HET MN A 499 1 HET MN A 500 1 HET GOL A 503 13 HET GOL A 504 14 HET GOL A 505 14 HET MN B 499 1 HET MN B 500 1 HET GOL B 503 13 HET GOL B 504 13 HET GOL B 505 13 HET GOL B 506 13 HETNAM MN MANGANESE (II) ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 MN 4(MN 2+) FORMUL 5 GOL 7(C3 H8 O3) FORMUL 14 HOH *779(H2 O) HELIX 1 AA1 LEU A 20 LYS A 36 1 17 HELIX 2 AA2 GLU A 68 GLY A 76 1 9 HELIX 3 AA3 PRO A 101 SER A 103 5 3 HELIX 4 AA4 HIS A 104 GLY A 109 1 6 HELIX 5 AA5 SER A 113 ALA A 122 1 10 HELIX 6 AA6 GLU A 131 GLN A 139 1 9 HELIX 7 AA7 GLY A 165 PHE A 169 5 5 HELIX 8 AA8 ILE A 175 PHE A 186 1 12 HELIX 9 AA9 THR A 188 VAL A 213 1 26 HELIX 10 AB1 LYS A 218 GLY A 235 1 18 HELIX 11 AB2 GLU A 249 VAL A 253 5 5 HELIX 12 AB3 THR A 299 MET A 320 1 22 HELIX 13 AB4 TRP A 325 MET A 344 1 20 HELIX 14 AB5 SER A 350 ALA A 357 1 8 HELIX 15 AB6 LEU A 359 MET A 364 1 6 HELIX 16 AB7 GLY A 393 LEU A 397 5 5 HELIX 17 AB8 ILE A 418 ALA A 427 1 10 HELIX 18 AB9 ASP A 428 SER A 433 1 6 HELIX 19 AC1 ASN A 436 ARG A 444 1 9 HELIX 20 AC2 THR A 471 ALA A 480 1 10 HELIX 21 AC3 LEU B 20 ASN B 37 1 18 HELIX 22 AC4 GLU B 68 GLY B 76 1 9 HELIX 23 AC5 PRO B 101 SER B 103 5 3 HELIX 24 AC6 HIS B 104 GLY B 109 1 6 HELIX 25 AC7 SER B 113 ALA B 122 1 10 HELIX 26 AC8 GLU B 131 LYS B 140 1 10 HELIX 27 AC9 GLY B 165 PHE B 169 5 5 HELIX 28 AD1 ILE B 175 PHE B 186 1 12 HELIX 29 AD2 THR B 188 VAL B 213 1 26 HELIX 30 AD3 LYS B 218 GLY B 235 1 18 HELIX 31 AD4 GLU B 249 VAL B 253 5 5 HELIX 32 AD5 THR B 299 MET B 320 1 22 HELIX 33 AD6 TRP B 325 MET B 344 1 20 HELIX 34 AD7 SER B 350 ALA B 357 1 8 HELIX 35 AD8 LEU B 359 MET B 364 1 6 HELIX 36 AD9 GLY B 393 LEU B 397 5 5 HELIX 37 AE1 ILE B 418 ALA B 427 1 10 HELIX 38 AE2 ASP B 428 SER B 433 1 6 HELIX 39 AE3 ASN B 436 GLN B 441 1 6 HELIX 40 AE4 ARG B 442 ARG B 444 5 3 HELIX 41 AE5 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 VAL A 46 O ILE A 86 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 2 THR A 54 GLN A 55 0 SHEET 2 AA3 2 GLY A 62 VAL A 63 -1 O VAL A 63 N THR A 54 SHEET 1 AA4 2 HIS A 238 SER A 239 0 SHEET 2 AA4 2 GLY A 279 GLU A 280 -1 O GLU A 280 N HIS A 238 SHEET 1 AA5 3 ILE A 244 SER A 247 0 SHEET 2 AA5 3 MET A 272 MET A 277 -1 O LEU A 274 N GLY A 246 SHEET 3 AA5 3 ILE A 288 PRO A 293 -1 O PHE A 292 N CYS A 273 SHEET 1 AA6 3 VAL A 408 VAL A 411 0 SHEET 2 AA6 3 GLU A 453 VAL A 457 -1 O VAL A 455 N LEU A 409 SHEET 3 AA6 3 ILE A 462 LEU A 464 -1 O GLU A 463 N VAL A 456 SHEET 1 AA7 2 GLY A 414 TYR A 416 0 SHEET 2 AA7 2 GLY A 448 ARG A 450 -1 O VAL A 449 N ILE A 415 SHEET 1 AA8 2 SER B 8 PHE B 9 0 SHEET 2 AA8 2 VAL B 18 PRO B 19 -1 O VAL B 18 N PHE B 9 SHEET 1 AA9 6 ASP B 125 TYR B 128 0 SHEET 2 AA9 6 SER B 93 VAL B 97 1 N VAL B 97 O GLN B 127 SHEET 3 AA9 6 TYR B 83 ASP B 87 -1 N TYR B 83 O PHE B 96 SHEET 4 AA9 6 ILE B 45 GLN B 49 -1 N LEU B 48 O GLY B 84 SHEET 5 AA9 6 LEU B 144 LEU B 145 1 O LEU B 145 N ILE B 45 SHEET 6 AA9 6 VAL B 171 ASN B 172 1 O ASN B 172 N LEU B 144 SHEET 1 AB1 2 THR B 54 GLN B 55 0 SHEET 2 AB1 2 GLY B 62 VAL B 63 -1 O VAL B 63 N THR B 54 SHEET 1 AB2 2 HIS B 238 SER B 239 0 SHEET 2 AB2 2 GLY B 279 GLU B 280 -1 O GLU B 280 N HIS B 238 SHEET 1 AB3 3 ILE B 244 SER B 247 0 SHEET 2 AB3 3 MET B 272 MET B 277 -1 O LEU B 274 N GLY B 246 SHEET 3 AB3 3 ILE B 288 PRO B 293 -1 O PHE B 292 N CYS B 273 SHEET 1 AB4 3 VAL B 408 VAL B 411 0 SHEET 2 AB4 3 GLU B 453 VAL B 457 -1 O GLU B 453 N VAL B 411 SHEET 3 AB4 3 ILE B 462 LEU B 464 -1 O GLU B 463 N VAL B 456 SHEET 1 AB5 2 GLY B 414 TYR B 416 0 SHEET 2 AB5 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 2.03 SSBOND 2 CYS B 482 CYS B 482 1555 3555 2.03 LINK OD1 ASP A 276 MN MN A 500 1555 1555 2.36 LINK OD2 ASP A 276 MN MN A 500 1555 1555 2.19 LINK OD2 ASP A 287 MN MN A 499 1555 1555 2.30 LINK OD1 ASP A 287 MN MN A 500 1555 1555 2.18 LINK NE2 HIS A 370 MN MN A 499 1555 1555 2.24 LINK OE2 GLU A 412 MN MN A 499 1555 1555 2.29 LINK OE2 GLU A 452 MN MN A 499 1555 1555 2.40 LINK OE1 GLU A 452 MN MN A 500 1555 1555 2.22 LINK MN MN A 500 O HOH A 915 1555 1555 2.69 LINK OD1 ASP B 276 MN MN B 500 1555 1555 2.26 LINK OD2 ASP B 276 MN MN B 500 1555 1555 2.05 LINK OD2 ASP B 287 MN MN B 499 1555 1555 2.42 LINK OD1 ASP B 287 MN MN B 500 1555 1555 2.11 LINK NE2 HIS B 370 MN MN B 499 1555 1555 2.34 LINK OE2 GLU B 412 MN MN B 499 1555 1555 2.36 LINK OE2 GLU B 452 MN MN B 499 1555 1555 2.35 LINK OE1 GLU B 452 MN MN B 500 1555 1555 2.21 LINK MN MN B 500 O HOH B 910 1555 1555 2.70 SITE 1 AC1 5 ASP A 287 HIS A 370 GLU A 412 GLU A 452 SITE 2 AC1 5 MN A 500 SITE 1 AC2 7 TYR A 241 ASP A 276 ASP A 287 THR A 289 SITE 2 AC2 7 GLU A 452 MN A 499 HOH A 915 SITE 1 AC3 7 LYS A 211 VAL A 213 LYS A 214 MET A 479 SITE 2 AC3 7 HOH A 602 HOH A 605 HOH A 608 SITE 1 AC4 5 GLN A 41 TRP A 325 GLY A 385 GLU A 387 SITE 2 AC4 5 ALA A 400 SITE 1 AC5 6 THR A 152 VAL A 386 GLU A 387 ARG A 388 SITE 2 AC5 6 HOH A 601 HOH A 692 SITE 1 AC6 5 ASP B 287 HIS B 370 GLU B 412 GLU B 452 SITE 2 AC6 5 MN B 500 SITE 1 AC7 7 TYR B 241 ASP B 276 ASP B 287 THR B 289 SITE 2 AC7 7 GLU B 452 MN B 499 HOH B 910 SITE 1 AC8 5 SER B 313 ARG B 314 MET B 317 GLU B 453 SITE 2 AC8 5 HOH B 606 SITE 1 AC9 7 GLU B 249 PHE B 417 ILE B 418 ASP B 419 SITE 2 AC9 7 GLY B 445 HOH B 607 HOH B 708 SITE 1 AD1 5 ASP A 264 PHE B 9 TRP B 10 LEU B 11 SITE 2 AD1 5 HOH B 602 SITE 1 AD2 4 PHE B 163 GLY B 165 ILE B 166 SER B 167 CRYST1 103.555 108.533 211.804 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 0.009657 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009214 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004721 0.00000