HEADER HYDROLASE 01-OCT-15 5E33 TITLE STRUCTURE OF HUMAN DPP3 IN COMPLEX WITH MET-ENKEPHALIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIPEPTIDYL PEPTIDASE 3; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DIPEPTIDYL AMINOPEPTIDASE III,DIPEPTIDYL ARYLAMIDASE III, COMPND 5 DIPEPTIDYL PEPTIDASE III,DPP III,ENKEPHALINASE B; COMPND 6 EC: 3.4.14.4; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: MET-ENKEPHALIN; COMPND 11 CHAIN: B; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: DPP3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28MHL; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 14 ORGANISM_TAXID: 9606 KEYWDS COMPLEX, OPIOID-PEPTIDE, ZINC-HYDROLASE, PEPTIDASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR P.KUMAR,V.REITHOFER,M.REISINGER,T.PAVKOV-KELLER,S.WALLNER, AUTHOR 2 P.MACHEROUX,K.GRUBER REVDAT 3 10-JAN-24 5E33 1 ATOM REVDAT 2 06-SEP-17 5E33 1 ATOM REVDAT 1 13-APR-16 5E33 0 JRNL AUTH P.KUMAR,V.REITHOFER,M.REISINGER,S.WALLNER,T.PAVKOV-KELLER, JRNL AUTH 2 P.MACHEROUX,K.GRUBER JRNL TITL SUBSTRATE COMPLEXES OF HUMAN DIPEPTIDYL PEPTIDASE III REVEAL JRNL TITL 2 THE MECHANISM OF ENZYME INHIBITION. JRNL REF SCI REP V. 6 23787 2016 JRNL REFN ESSN 2045-2322 JRNL PMID 27025154 JRNL DOI 10.1038/SREP23787 REMARK 2 REMARK 2 RESOLUTION. 1.84 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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) : 1.84 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.42 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 3 NUMBER OF REFLECTIONS : 68229 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3411 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 45.4300 - 5.2975 0.99 2822 147 0.1507 0.1781 REMARK 3 2 5.2975 - 4.2058 1.00 2800 147 0.1463 0.1755 REMARK 3 3 4.2058 - 3.6744 0.98 2778 147 0.1542 0.1863 REMARK 3 4 3.6744 - 3.3386 0.99 2760 145 0.1715 0.2349 REMARK 3 5 3.3386 - 3.0993 0.99 2748 145 0.1797 0.2056 REMARK 3 6 3.0993 - 2.9166 0.99 2783 146 0.1905 0.2589 REMARK 3 7 2.9166 - 2.7706 1.00 2764 146 0.1952 0.2389 REMARK 3 8 2.7706 - 2.6500 0.98 2743 144 0.1969 0.2268 REMARK 3 9 2.6500 - 2.5480 0.99 2788 147 0.1845 0.2324 REMARK 3 10 2.5480 - 2.4601 0.99 2743 144 0.1871 0.2075 REMARK 3 11 2.4601 - 2.3832 0.98 2751 145 0.1842 0.2501 REMARK 3 12 2.3832 - 2.3150 0.99 2783 146 0.1791 0.2436 REMARK 3 13 2.3150 - 2.2541 0.96 2664 141 0.1919 0.2442 REMARK 3 14 2.2541 - 2.1991 0.92 2551 134 0.2093 0.2602 REMARK 3 15 2.1991 - 2.1491 0.99 2725 144 0.1846 0.2510 REMARK 3 16 2.1491 - 2.1034 0.99 2732 143 0.1951 0.2172 REMARK 3 17 2.1034 - 2.0613 0.95 2665 141 0.2182 0.3002 REMARK 3 18 2.0613 - 2.0224 0.96 2690 141 0.2191 0.2600 REMARK 3 19 2.0224 - 1.9863 0.97 2681 142 0.2205 0.2746 REMARK 3 20 1.9863 - 1.9526 0.98 2691 141 0.2443 0.2655 REMARK 3 21 1.9526 - 1.9211 0.90 2530 133 0.3073 0.3704 REMARK 3 22 1.9211 - 1.8916 0.87 2415 127 0.3490 0.4328 REMARK 3 23 1.8916 - 1.8637 0.95 2605 138 0.3116 0.3101 REMARK 3 24 1.8637 - 1.8375 0.92 2606 137 0.2840 0.3378 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) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.350 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 30.13 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.00 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 : 0.011 5957 REMARK 3 ANGLE : 1.175 8070 REMARK 3 CHIRALITY : 0.056 867 REMARK 3 PLANARITY : 0.006 1061 REMARK 3 DIHEDRAL : 14.622 2204 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 5E33 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-OCT-15. REMARK 100 THE DEPOSITION ID IS D_1000214271. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-APR-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.2 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.972390 REMARK 200 MONOCHROMATOR : LIQUID NITROGEN COOLED CHANNEL REMARK 200 -CUT SILICON MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 68276 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.830 REMARK 200 RESOLUTION RANGE LOW (A) : 45.420 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.05052 REMARK 200 R SYM (I) : 0.05052 REMARK 200 FOR THE DATA SET : 14.7800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.83 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.73600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.750 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX 1.9_1692 REMARK 200 STARTING MODEL: 3T6B REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.04 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.51 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.056M SODIUM PHOSPHATE MONOBASIC REMARK 280 MONOHYDRATE, 1.344M POTASSIUM PHOSPAHTE DIBASIC, PH- 8.2, PH 8.2, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 59.89500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 52.88000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 59.89500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 52.88000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1870 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26850 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -63.0 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 A1180 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 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 NH2 ARG A 68 OE2 GLU A 712 2.05 REMARK 500 OD1 ASP A 464 N LYS A 466 2.15 REMARK 500 NH2 ARG A 68 OE2 GLU A 712 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 1273 O HOH A 1339 2757 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 319 NE - CZ - NH1 ANGL. DEV. = -3.0 DEGREES REMARK 500 LYS A 466 N - CA - C ANGL. DEV. = -16.9 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 THR A 52 -62.40 -106.75 REMARK 500 PRO A 358 28.72 -76.03 REMARK 500 TYR A 417 42.71 -89.20 REMARK 500 SER A 500 -106.86 30.68 REMARK 500 PHE A 530 -34.33 -137.65 REMARK 500 GLU A 531 49.12 31.13 REMARK 500 ASP A 707 24.97 -148.63 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 A1417 DISTANCE = 6.42 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 802 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 102 OD1 REMARK 620 2 SER A 108 OG 65.3 REMARK 620 3 SER A 384 O 86.1 68.2 REMARK 620 4 HOH A1278 O 87.4 137.9 144.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 803 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 164 O REMARK 620 2 GLY A 167 O 80.1 REMARK 620 3 HOH A1028 O 154.0 98.7 REMARK 620 4 HOH A1156 O 98.6 176.0 84.1 REMARK 620 5 HOH A1239 O 76.2 84.4 77.8 99.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 804 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 317 O REMARK 620 2 SER A 317 OG 64.6 REMARK 620 3 GLY A 323 O 83.0 74.9 REMARK 620 4 ASP A 496 OD1 143.8 79.9 80.6 REMARK 620 5 SER A 504 OG 79.3 104.3 160.5 118.7 REMARK 620 6 HOH A1009 O 92.3 155.5 95.2 121.2 77.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 801 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 450 NE2 REMARK 620 2 HIS A 455 NE2 96.8 REMARK 620 3 GLU A 508 OE1 98.8 100.7 REMARK 620 4 HOH A1329 O 88.9 99.9 157.0 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 ZN A 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 802 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 803 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K A 804 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3FVY RELATED DB: PDB REMARK 900 CONTAINS THE SAME STRUCTURE IN ITS UNBOUND FORM REMARK 900 RELATED ID: 3T6B RELATED DB: PDB REMARK 900 CONTAINS THE SAME PROTEIN IN ITS BOUND FORM DBREF 5E33 A 1 726 UNP Q9NY33 DPP3_HUMAN 1 726 DBREF 5E33 B 1 5 PDB 5E33 5E33 1 5 SEQADV 5E33 SER A 19 UNP Q9NY33 CYS 19 ENGINEERED MUTATION SEQADV 5E33 CYS A 207 UNP Q9NY33 GLU 207 ENGINEERED MUTATION SEQADV 5E33 ALA A 451 UNP Q9NY33 GLU 451 ENGINEERED MUTATION SEQADV 5E33 CYS A 491 UNP Q9NY33 SER 491 ENGINEERED MUTATION SEQADV 5E33 SER A 519 UNP Q9NY33 CYS 519 ENGINEERED MUTATION SEQADV 5E33 SER A 654 UNP Q9NY33 CYS 654 ENGINEERED MUTATION SEQRES 1 A 726 MET ALA ASP THR GLN TYR ILE LEU PRO ASN ASP ILE GLY SEQRES 2 A 726 VAL SER SER LEU ASP SER ARG GLU ALA PHE ARG LEU LEU SEQRES 3 A 726 SER PRO THR GLU ARG LEU TYR ALA TYR HIS LEU SER ARG SEQRES 4 A 726 ALA ALA TRP TYR GLY GLY LEU ALA VAL LEU LEU GLN THR SEQRES 5 A 726 SER PRO GLU ALA PRO TYR ILE TYR ALA LEU LEU SER ARG SEQRES 6 A 726 LEU PHE ARG ALA GLN ASP PRO ASP GLN LEU ARG GLN HIS SEQRES 7 A 726 ALA LEU ALA GLU GLY LEU THR GLU GLU GLU TYR GLN ALA SEQRES 8 A 726 PHE LEU VAL TYR ALA ALA GLY VAL TYR SER ASN MET GLY SEQRES 9 A 726 ASN TYR LYS SER PHE GLY ASP THR LYS PHE VAL PRO ASN SEQRES 10 A 726 LEU PRO LYS GLU LYS LEU GLU ARG VAL ILE LEU GLY SER SEQRES 11 A 726 GLU ALA ALA GLN GLN HIS PRO GLU GLU VAL ARG GLY LEU SEQRES 12 A 726 TRP GLN THR CYS GLY GLU LEU MET PHE SER LEU GLU PRO SEQRES 13 A 726 ARG LEU ARG HIS LEU GLY LEU GLY LYS GLU GLY ILE THR SEQRES 14 A 726 THR TYR PHE SER GLY ASN CYS THR MET GLU ASP ALA LYS SEQRES 15 A 726 LEU ALA GLN ASP PHE LEU ASP SER GLN ASN LEU SER ALA SEQRES 16 A 726 TYR ASN THR ARG LEU PHE LYS GLU VAL ASP GLY CYS GLY SEQRES 17 A 726 LYS PRO TYR TYR GLU VAL ARG LEU ALA SER VAL LEU GLY SEQRES 18 A 726 SER GLU PRO SER LEU ASP SER GLU VAL THR SER LYS LEU SEQRES 19 A 726 LYS SER TYR GLU PHE ARG GLY SER PRO PHE GLN VAL THR SEQRES 20 A 726 ARG GLY ASP TYR ALA PRO ILE LEU GLN LYS VAL VAL GLU SEQRES 21 A 726 GLN LEU GLU LYS ALA LYS ALA TYR ALA ALA ASN SER HIS SEQRES 22 A 726 GLN GLY GLN MET LEU ALA GLN TYR ILE GLU SER PHE THR SEQRES 23 A 726 GLN GLY SER ILE GLU ALA HIS LYS ARG GLY SER ARG PHE SEQRES 24 A 726 TRP ILE GLN ASP LYS GLY PRO ILE VAL GLU SER TYR ILE SEQRES 25 A 726 GLY PHE ILE GLU SER TYR ARG ASP PRO PHE GLY SER ARG SEQRES 26 A 726 GLY GLU PHE GLU GLY PHE VAL ALA VAL VAL ASN LYS ALA SEQRES 27 A 726 MET SER ALA LYS PHE GLU ARG LEU VAL ALA SER ALA GLU SEQRES 28 A 726 GLN LEU LEU LYS GLU LEU PRO TRP PRO PRO THR PHE GLU SEQRES 29 A 726 LYS ASP LYS PHE LEU THR PRO ASP PHE THR SER LEU ASP SEQRES 30 A 726 VAL LEU THR PHE ALA GLY SER GLY ILE PRO ALA GLY ILE SEQRES 31 A 726 ASN ILE PRO ASN TYR ASP ASP LEU ARG GLN THR GLU GLY SEQRES 32 A 726 PHE LYS ASN VAL SER LEU GLY ASN VAL LEU ALA VAL ALA SEQRES 33 A 726 TYR ALA THR GLN ARG GLU LYS LEU THR PHE LEU GLU GLU SEQRES 34 A 726 ASP ASP LYS ASP LEU TYR ILE LEU TRP LYS GLY PRO SER SEQRES 35 A 726 PHE ASP VAL GLN VAL GLY LEU HIS ALA LEU LEU GLY HIS SEQRES 36 A 726 GLY SER GLY LYS LEU PHE VAL GLN ASP GLU LYS GLY ALA SEQRES 37 A 726 PHE ASN PHE ASP GLN GLU THR VAL ILE ASN PRO GLU THR SEQRES 38 A 726 GLY GLU GLN ILE GLN SER TRP TYR ARG CYS GLY GLU THR SEQRES 39 A 726 TRP ASP SER LYS PHE SER THR ILE ALA SER SER TYR GLU SEQRES 40 A 726 GLU CYS ARG ALA GLU SER VAL GLY LEU TYR LEU SER LEU SEQRES 41 A 726 HIS PRO GLN VAL LEU GLU ILE PHE GLY PHE GLU GLY ALA SEQRES 42 A 726 ASP ALA GLU ASP VAL ILE TYR VAL ASN TRP LEU ASN MET SEQRES 43 A 726 VAL ARG ALA GLY LEU LEU ALA LEU GLU PHE TYR THR PRO SEQRES 44 A 726 GLU ALA PHE ASN TRP ARG GLN ALA HIS MET GLN ALA ARG SEQRES 45 A 726 PHE VAL ILE LEU ARG VAL LEU LEU GLU ALA GLY GLU GLY SEQRES 46 A 726 LEU VAL THR ILE THR PRO THR THR GLY SER ASP GLY ARG SEQRES 47 A 726 PRO ASP ALA ARG VAL ARG LEU ASP ARG SER LYS ILE ARG SEQRES 48 A 726 SER VAL GLY LYS PRO ALA LEU GLU ARG PHE LEU ARG ARG SEQRES 49 A 726 LEU GLN VAL LEU LYS SER THR GLY ASP VAL ALA GLY GLY SEQRES 50 A 726 ARG ALA LEU TYR GLU GLY TYR ALA THR VAL THR ASP ALA SEQRES 51 A 726 PRO PRO GLU SER PHE LEU THR LEU ARG ASP THR VAL LEU SEQRES 52 A 726 LEU ARG LYS GLU SER ARG LYS LEU ILE VAL GLN PRO ASN SEQRES 53 A 726 THR ARG LEU GLU GLY SER ASP VAL GLN LEU LEU GLU TYR SEQRES 54 A 726 GLU ALA SER ALA ALA GLY LEU ILE ARG SER PHE SER GLU SEQRES 55 A 726 ARG PHE PRO GLU ASP GLY PRO GLU LEU GLU GLU ILE LEU SEQRES 56 A 726 THR GLN LEU ALA THR ALA ASP ALA ARG PHE TRP SEQRES 1 B 5 TYR GLY GLY PHE MET HET ZN A 801 1 HET MG A 802 1 HET MG A 803 1 HET K A 804 1 HETNAM ZN ZINC ION HETNAM MG MAGNESIUM ION HETNAM K POTASSIUM ION FORMUL 3 ZN ZN 2+ FORMUL 4 MG 2(MG 2+) FORMUL 6 K K 1+ FORMUL 7 HOH *519(H2 O) HELIX 1 AA1 SER A 19 LEU A 26 1 8 HELIX 2 AA2 SER A 27 GLN A 51 1 25 HELIX 3 AA3 GLU A 55 GLN A 70 1 16 HELIX 4 AA4 ASP A 71 GLU A 82 1 12 HELIX 5 AA5 THR A 85 MET A 103 1 19 HELIX 6 AA6 PRO A 119 GLY A 129 1 11 HELIX 7 AA7 SER A 130 HIS A 136 1 7 HELIX 8 AA8 HIS A 136 SER A 153 1 18 HELIX 9 AA9 GLU A 155 ARG A 159 5 5 HELIX 10 AB1 THR A 177 GLN A 191 1 15 HELIX 11 AB2 VAL A 230 LEU A 234 5 5 HELIX 12 AB3 TYR A 251 ALA A 267 1 17 HELIX 13 AB4 ASN A 271 GLY A 288 1 18 HELIX 14 AB5 SER A 289 ASP A 303 1 15 HELIX 15 AB6 ASN A 336 VAL A 347 1 12 HELIX 16 AB7 SER A 349 LEU A 354 1 6 HELIX 17 AB8 LYS A 355 LEU A 357 5 3 HELIX 18 AB9 PRO A 360 GLU A 364 5 5 HELIX 19 AC1 TYR A 395 GLU A 402 1 8 HELIX 20 AC2 GLY A 410 TYR A 417 1 8 HELIX 21 AC3 GLU A 428 LEU A 453 1 26 HELIX 22 AC4 THR A 494 SER A 500 1 7 HELIX 23 AC5 ILE A 502 SER A 519 1 18 HELIX 24 AC6 GLN A 523 PHE A 528 1 6 HELIX 25 AC7 GLY A 532 ALA A 553 1 22 HELIX 26 AC8 GLN A 566 ALA A 582 1 17 HELIX 27 AC9 ARG A 607 ILE A 610 5 4 HELIX 28 AD1 VAL A 613 THR A 631 1 19 HELIX 29 AD2 ASP A 633 ALA A 645 1 13 HELIX 30 AD3 SER A 654 ARG A 665 1 12 HELIX 31 AD4 SER A 692 GLU A 702 1 11 HELIX 32 AD5 ASP A 707 ASP A 722 1 16 HELIX 33 AD6 ALA A 723 TRP A 726 5 4 SHEET 1 AA1 2 VAL A 14 SER A 16 0 SHEET 2 AA1 2 LEU A 671 VAL A 673 1 O VAL A 673 N SER A 15 SHEET 1 AA2 4 THR A 198 VAL A 204 0 SHEET 2 AA2 4 PRO A 210 ALA A 217 -1 O GLU A 213 N PHE A 201 SHEET 3 AA2 4 SER A 242 ASP A 250 1 O THR A 247 N LEU A 216 SHEET 4 AA2 4 SER A 236 PHE A 239 -1 N TYR A 237 O PHE A 244 SHEET 1 AA3 6 VAL A 308 GLU A 316 0 SHEET 2 AA3 6 GLU A 327 VAL A 335 -1 O ALA A 333 N GLU A 309 SHEET 3 AA3 6 ASP A 372 ALA A 382 -1 O LEU A 379 N VAL A 332 SHEET 4 AA3 6 LYS A 405 LEU A 409 1 O ASN A 406 N ASP A 372 SHEET 5 AA3 6 GLY A 389 ILE A 392 -1 N ILE A 392 O LYS A 405 SHEET 6 AA3 6 GLY B 2 GLY B 3 -1 O GLY B 3 N GLY A 389 SHEET 1 AA4 2 TYR A 557 THR A 558 0 SHEET 2 AA4 2 ASN A 563 TRP A 564 -1 O ASN A 563 N THR A 558 SHEET 1 AA5 2 VAL A 587 THR A 593 0 SHEET 2 AA5 2 PRO A 599 LEU A 605 -1 O ASP A 600 N THR A 592 SHEET 1 AA6 2 ASN A 676 GLU A 680 0 SHEET 2 AA6 2 ASP A 683 LEU A 687 -1 O LEU A 687 N ASN A 676 SSBOND 1 CYS A 207 CYS A 207 1555 2857 2.04 LINK OD1 ASN A 102 MG MG A 802 1555 1555 2.95 LINK OG SER A 108 MG MG A 802 1555 1555 2.89 LINK O GLY A 164 MG MG A 803 1555 1555 2.71 LINK O GLY A 167 MG MG A 803 1555 1555 2.55 LINK O SER A 317 K K A 804 1555 1555 3.00 LINK OG SER A 317 K K A 804 1555 1555 2.70 LINK O GLY A 323 K K A 804 1555 1555 2.60 LINK O SER A 384 MG MG A 802 1555 1555 2.58 LINK NE2 HIS A 450 ZN ZN A 801 1555 1555 1.99 LINK NE2 HIS A 455 ZN ZN A 801 1555 1555 2.07 LINK OD1 ASP A 496 K K A 804 1555 1555 2.88 LINK OG SER A 504 K K A 804 1555 1555 2.66 LINK OE1 GLU A 508 ZN ZN A 801 1555 1555 2.13 LINK ZN ZN A 801 O HOH A1329 1555 1555 2.51 LINK MG MG A 802 O HOH A1278 1555 1555 2.68 LINK MG MG A 803 O HOH A1028 1555 1555 2.82 LINK MG MG A 803 O HOH A1156 1555 1555 2.81 LINK MG MG A 803 O HOH A1239 1555 1555 2.88 LINK K K A 804 O HOH A1009 1555 1555 3.01 CISPEP 1 ILE A 392 PRO A 393 0 -0.70 CISPEP 2 PRO A 651 PRO A 652 0 2.71 SITE 1 AC1 5 HIS A 450 HIS A 455 GLU A 508 HOH A1329 SITE 2 AC1 5 GLY B 2 SITE 1 AC2 6 SER A 101 ASN A 102 SER A 108 SER A 384 SITE 2 AC2 6 GLY A 385 HOH A1278 SITE 1 AC3 6 GLY A 162 GLY A 164 GLY A 167 HOH A1028 SITE 2 AC3 6 HOH A1156 HOH A1239 SITE 1 AC4 5 SER A 317 GLY A 323 ASP A 496 SER A 504 SITE 2 AC4 5 HOH A1009 CRYST1 119.790 105.760 65.167 90.00 93.49 90.00 C 1 2 1 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.008348 0.000000 0.000509 0.00000 SCALE2 0.000000 0.009455 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015374 0.00000