HEADER HYDROLASE/VIRAL PROTEIN 13-JUN-13 4L72 TITLE CRYSTAL STRUCTURE OF MERS-COV COMPLEXED WITH HUMAN DPP4 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIPEPTIDYL PEPTIDASE 4; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 39-766; COMPND 5 SYNONYM: ADABP, ADENOSINE DEAMINASE COMPLEXING PROTEIN 2, ADCP-2, COMPND 6 DIPEPTIDYL PEPTIDASE IV, DPP IV, T-CELL ACTIVATION ANTIGEN CD26, COMPND 7 TP103, DIPEPTIDYL PEPTIDASE 4 MEMBRANE FORM, DIPEPTIDYL PEPTIDASE IV COMPND 8 MEMBRANE FORM, DIPEPTIDYL PEPTIDASE 4 SOLUBLE FORM, DIPEPTIDYL COMPND 9 PEPTIDASE IV SOLUBLE FORM; COMPND 10 EC: 3.4.14.5; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 2; COMPND 13 MOLECULE: MERS-COV RBD; COMPND 14 CHAIN: B; COMPND 15 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: DPP4, ADCP2, CD26; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: MIDDLE EAST RESPIRATORY SYNDROME CORONAVIRUS; SOURCE 10 ORGANISM_COMMON: MERS-COV; SOURCE 11 ORGANISM_TAXID: 1335626; SOURCE 12 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 7108 KEYWDS ALPHA/BETA HYDROLASE BETA-PROPELLER, GLYCOLATION, VIRUS RECEPTOR- KEYWDS 2 BINDING DOMAIN, HYDROLASE-VIRAL PROTEIN COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR X.Q.WANG,N.S.WANG REVDAT 6 13-NOV-24 4L72 1 REMARK REVDAT 5 08-NOV-23 4L72 1 HETSYN REVDAT 4 29-JUL-20 4L72 1 COMPND REMARK HETNAM LINK REVDAT 4 2 1 SITE ATOM REVDAT 3 22-JUL-15 4L72 1 SOURCE REVDAT 2 04-SEP-13 4L72 1 JRNL REVDAT 1 21-AUG-13 4L72 0 JRNL AUTH N.WANG,X.SHI,L.JIANG,S.ZHANG,D.WANG,P.TONG,D.GUO,L.FU,Y.CUI, JRNL AUTH 2 X.LIU,K.C.ARLEDGE,Y.H.CHEN,L.ZHANG,X.WANG JRNL TITL STRUCTURE OF MERS-COV SPIKE RECEPTOR-BINDING DOMAIN JRNL TITL 2 COMPLEXED WITH HUMAN RECEPTOR DPP4 JRNL REF CELL RES. V. 23 986 2013 JRNL REFN ISSN 1001-0602 JRNL PMID 23835475 JRNL DOI 10.1038/CR.2013.92 REMARK 2 REMARK 2 RESOLUTION. 3.01 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.1_1168) 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) : 3.01 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.90 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 39446 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.208 REMARK 3 R VALUE (WORKING SET) : 0.205 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1978 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 48.9931 - 7.2360 0.99 2977 168 0.2092 0.2331 REMARK 3 2 7.2360 - 5.7463 1.00 2775 144 0.2218 0.2760 REMARK 3 3 5.7463 - 5.0208 1.00 2705 146 0.1917 0.2372 REMARK 3 4 5.0208 - 4.5621 1.00 2702 144 0.1658 0.2283 REMARK 3 5 4.5621 - 4.2353 1.00 2676 140 0.1712 0.2128 REMARK 3 6 4.2353 - 3.9857 1.00 2675 125 0.1886 0.2157 REMARK 3 7 3.9857 - 3.7862 1.00 2669 140 0.1950 0.2360 REMARK 3 8 3.7862 - 3.6214 1.00 2610 151 0.1985 0.2624 REMARK 3 9 3.6214 - 3.4820 1.00 2622 141 0.2155 0.2567 REMARK 3 10 3.4820 - 3.3619 1.00 2629 129 0.2242 0.2655 REMARK 3 11 3.3619 - 3.2568 1.00 2603 146 0.2317 0.2802 REMARK 3 12 3.2568 - 3.1637 1.00 2604 160 0.2481 0.3121 REMARK 3 13 3.1637 - 3.0805 1.00 2612 120 0.2491 0.3146 REMARK 3 14 3.0805 - 3.0050 0.99 2609 124 0.2695 0.3753 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) : 0.340 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.950 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.010 7933 REMARK 3 ANGLE : 1.413 10798 REMARK 3 CHIRALITY : 0.095 1185 REMARK 3 PLANARITY : 0.005 1355 REMARK 3 DIHEDRAL : 18.908 2882 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A REMARK 3 ORIGIN FOR THE GROUP (A): -11.4546 -47.2999 -17.1331 REMARK 3 T TENSOR REMARK 3 T11: -0.0357 T22: 0.2527 REMARK 3 T33: 0.1070 T12: 0.0854 REMARK 3 T13: -0.0462 T23: -0.0588 REMARK 3 L TENSOR REMARK 3 L11: 0.4844 L22: 0.3362 REMARK 3 L33: 0.5027 L12: -0.1719 REMARK 3 L13: 0.2498 L23: 0.1140 REMARK 3 S TENSOR REMARK 3 S11: -0.0110 S12: -0.1446 S13: -0.0431 REMARK 3 S21: 0.1543 S22: 0.0096 S23: 0.0293 REMARK 3 S31: 0.1166 S32: 0.1714 S33: -0.1877 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN B REMARK 3 ORIGIN FOR THE GROUP (A): -46.8511 -11.8088 -16.0439 REMARK 3 T TENSOR REMARK 3 T11: 0.2957 T22: 0.3012 REMARK 3 T33: 0.5597 T12: 0.1134 REMARK 3 T13: -0.0905 T23: -0.2688 REMARK 3 L TENSOR REMARK 3 L11: 0.0263 L22: 0.0473 REMARK 3 L33: 0.3053 L12: 0.0302 REMARK 3 L13: -0.0434 L23: -0.0535 REMARK 3 S TENSOR REMARK 3 S11: 0.0679 S12: -0.0805 S13: 0.2619 REMARK 3 S21: -0.0511 S22: -0.1669 S23: 0.3195 REMARK 3 S31: -0.2849 S32: -0.2670 S33: -0.0494 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 4L72 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-JUN-13. REMARK 100 THE DEPOSITION ID IS D_1000080262. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-APR-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39446 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 REMARK 200 RESOLUTION RANGE LOW (A) : 48.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 7.200 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 48.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: PHASES REMARK 200 STARTING MODEL: 2G63, 2AJF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 71.77 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG1500, PH 7.2, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 175.90433 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 351.80867 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 263.85650 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 439.76083 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 87.95217 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 175.90433 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 351.80867 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 439.76083 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 263.85650 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 87.95217 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C, D, E 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4320 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 58420 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C, D, E 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 350 BIOMT1 2 0.500000 -0.866025 0.000000 -55.30450 REMARK 350 BIOMT2 2 -0.866025 -0.500000 0.000000 -95.79020 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -87.95217 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 596 OD1 ASP A 678 2.12 REMARK 500 ND2 ASN A 85 C2 NAG A 801 2.19 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 LEU A 60 CA - CB - CG ANGL. DEV. = 14.3 DEGREES REMARK 500 LEU B 388 CA - CB - CG ANGL. DEV. = 14.8 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 66 13.45 -153.59 REMARK 500 LYS A 71 55.74 -109.11 REMARK 500 TYR A 83 -112.33 -123.72 REMARK 500 LEU A 90 118.39 -161.13 REMARK 500 TRP A 124 -112.10 -135.64 REMARK 500 HIS A 126 -11.39 95.68 REMARK 500 TYR A 128 -160.78 -170.56 REMARK 500 ASN A 138 -70.64 -60.70 REMARK 500 VAL A 207 -64.72 -122.62 REMARK 500 ALA A 213 46.76 -143.90 REMARK 500 SER A 242 -155.37 61.31 REMARK 500 SER A 275 32.49 -95.04 REMARK 500 GLN A 320 40.30 -73.03 REMARK 500 ALA A 342 -0.17 68.98 REMARK 500 LYS A 423 26.22 43.62 REMARK 500 ASN A 450 53.89 -166.09 REMARK 500 PHE A 534 106.15 -50.47 REMARK 500 LYS A 536 -15.75 -47.20 REMARK 500 TYR A 547 -61.47 -129.31 REMARK 500 GLN A 553 99.63 -163.52 REMARK 500 THR A 600 -96.14 -121.24 REMARK 500 ASN A 621 1.20 -67.53 REMARK 500 ARG A 623 62.56 -159.34 REMARK 500 SER A 630 -121.68 55.15 REMARK 500 PRO A 674 32.54 -87.72 REMARK 500 ASP A 678 -92.14 -115.46 REMARK 500 ASN A 710 -74.40 -93.88 REMARK 500 ILE A 742 45.67 38.60 REMARK 500 PHE B 385 113.51 -27.85 REMARK 500 PRO B 387 14.68 -64.56 REMARK 500 SER B 390 -105.37 -100.23 REMARK 500 THR B 405 -60.37 -103.11 REMARK 500 CYS B 407 -170.83 -171.46 REMARK 500 LEU B 414 53.82 -170.62 REMARK 500 LEU B 415 -25.28 -161.24 REMARK 500 ASN B 436 176.14 -56.69 REMARK 500 ALA B 461 40.47 -141.56 REMARK 500 ASN B 487 -71.83 -31.02 REMARK 500 ARG B 511 -52.90 -120.03 REMARK 500 LEU B 567 115.24 86.61 REMARK 500 ASP B 580 28.47 -167.59 REMARK 500 ASN B 582 80.98 -59.34 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 SER B 386 PRO B 387 147.33 REMARK 500 REMARK 500 REMARK: NULL DBREF 4L72 A 39 766 UNP P27487 DPP4_HUMAN 39 766 DBREF 4L72 B 382 585 PDB 4L72 4L72 382 585 SEQRES 1 A 728 SER ARG LYS THR TYR THR LEU THR ASP TYR LEU LYS ASN SEQRES 2 A 728 THR TYR ARG LEU LYS LEU TYR SER LEU ARG TRP ILE SER SEQRES 3 A 728 ASP HIS GLU TYR LEU TYR LYS GLN GLU ASN ASN ILE LEU SEQRES 4 A 728 VAL PHE ASN ALA GLU TYR GLY ASN SER SER VAL PHE LEU SEQRES 5 A 728 GLU ASN SER THR PHE ASP GLU PHE GLY HIS SER ILE ASN SEQRES 6 A 728 ASP TYR SER ILE SER PRO ASP GLY GLN PHE ILE LEU LEU SEQRES 7 A 728 GLU TYR ASN TYR VAL LYS GLN TRP ARG HIS SER TYR THR SEQRES 8 A 728 ALA SER TYR ASP ILE TYR ASP LEU ASN LYS ARG GLN LEU SEQRES 9 A 728 ILE THR GLU GLU ARG ILE PRO ASN ASN THR GLN TRP VAL SEQRES 10 A 728 THR TRP SER PRO VAL GLY HIS LYS LEU ALA TYR VAL TRP SEQRES 11 A 728 ASN ASN ASP ILE TYR VAL LYS ILE GLU PRO ASN LEU PRO SEQRES 12 A 728 SER TYR ARG ILE THR TRP THR GLY LYS GLU ASP ILE ILE SEQRES 13 A 728 TYR ASN GLY ILE THR ASP TRP VAL TYR GLU GLU GLU VAL SEQRES 14 A 728 PHE SER ALA TYR SER ALA LEU TRP TRP SER PRO ASN GLY SEQRES 15 A 728 THR PHE LEU ALA TYR ALA GLN PHE ASN ASP THR GLU VAL SEQRES 16 A 728 PRO LEU ILE GLU TYR SER PHE TYR SER ASP GLU SER LEU SEQRES 17 A 728 GLN TYR PRO LYS THR VAL ARG VAL PRO TYR PRO LYS ALA SEQRES 18 A 728 GLY ALA VAL ASN PRO THR VAL LYS PHE PHE VAL VAL ASN SEQRES 19 A 728 THR ASP SER LEU SER SER VAL THR ASN ALA THR SER ILE SEQRES 20 A 728 GLN ILE THR ALA PRO ALA SER MET LEU ILE GLY ASP HIS SEQRES 21 A 728 TYR LEU CYS ASP VAL THR TRP ALA THR GLN GLU ARG ILE SEQRES 22 A 728 SER LEU GLN TRP LEU ARG ARG ILE GLN ASN TYR SER VAL SEQRES 23 A 728 MET ASP ILE CYS ASP TYR ASP GLU SER SER GLY ARG TRP SEQRES 24 A 728 ASN CYS LEU VAL ALA ARG GLN HIS ILE GLU MET SER THR SEQRES 25 A 728 THR GLY TRP VAL GLY ARG PHE ARG PRO SER GLU PRO HIS SEQRES 26 A 728 PHE THR LEU ASP GLY ASN SER PHE TYR LYS ILE ILE SER SEQRES 27 A 728 ASN GLU GLU GLY TYR ARG HIS ILE CYS TYR PHE GLN ILE SEQRES 28 A 728 ASP LYS LYS ASP CYS THR PHE ILE THR LYS GLY THR TRP SEQRES 29 A 728 GLU VAL ILE GLY ILE GLU ALA LEU THR SER ASP TYR LEU SEQRES 30 A 728 TYR TYR ILE SER ASN GLU TYR LYS GLY MET PRO GLY GLY SEQRES 31 A 728 ARG ASN LEU TYR LYS ILE GLN LEU SER ASP TYR THR LYS SEQRES 32 A 728 VAL THR CYS LEU SER CYS GLU LEU ASN PRO GLU ARG CYS SEQRES 33 A 728 GLN TYR TYR SER VAL SER PHE SER LYS GLU ALA LYS TYR SEQRES 34 A 728 TYR GLN LEU ARG CYS SER GLY PRO GLY LEU PRO LEU TYR SEQRES 35 A 728 THR LEU HIS SER SER VAL ASN ASP LYS GLY LEU ARG VAL SEQRES 36 A 728 LEU GLU ASP ASN SER ALA LEU ASP LYS MET LEU GLN ASN SEQRES 37 A 728 VAL GLN MET PRO SER LYS LYS LEU ASP PHE ILE ILE LEU SEQRES 38 A 728 ASN GLU THR LYS PHE TRP TYR GLN MET ILE LEU PRO PRO SEQRES 39 A 728 HIS PHE ASP LYS SER LYS LYS TYR PRO LEU LEU LEU ASP SEQRES 40 A 728 VAL TYR ALA GLY PRO CYS SER GLN LYS ALA ASP THR VAL SEQRES 41 A 728 PHE ARG LEU ASN TRP ALA THR TYR LEU ALA SER THR GLU SEQRES 42 A 728 ASN ILE ILE VAL ALA SER PHE ASP GLY ARG GLY SER GLY SEQRES 43 A 728 TYR GLN GLY ASP LYS ILE MET HIS ALA ILE ASN ARG ARG SEQRES 44 A 728 LEU GLY THR PHE GLU VAL GLU ASP GLN ILE GLU ALA ALA SEQRES 45 A 728 ARG GLN PHE SER LYS MET GLY PHE VAL ASP ASN LYS ARG SEQRES 46 A 728 ILE ALA ILE TRP GLY TRP SER TYR GLY GLY TYR VAL THR SEQRES 47 A 728 SER MET VAL LEU GLY SER GLY SER GLY VAL PHE LYS CYS SEQRES 48 A 728 GLY ILE ALA VAL ALA PRO VAL SER ARG TRP GLU TYR TYR SEQRES 49 A 728 ASP SER VAL TYR THR GLU ARG TYR MET GLY LEU PRO THR SEQRES 50 A 728 PRO GLU ASP ASN LEU ASP HIS TYR ARG ASN SER THR VAL SEQRES 51 A 728 MET SER ARG ALA GLU ASN PHE LYS GLN VAL GLU TYR LEU SEQRES 52 A 728 LEU ILE HIS GLY THR ALA ASP ASP ASN VAL HIS PHE GLN SEQRES 53 A 728 GLN SER ALA GLN ILE SER LYS ALA LEU VAL ASP VAL GLY SEQRES 54 A 728 VAL ASP PHE GLN ALA MET TRP TYR THR ASP GLU ASP HIS SEQRES 55 A 728 GLY ILE ALA SER SER THR ALA HIS GLN HIS ILE TYR THR SEQRES 56 A 728 HIS MET SER HIS PHE ILE LYS GLN CYS PHE SER LEU PRO SEQRES 1 B 204 GLU CYS ASP PHE SER PRO LEU LEU SER GLY THR PRO PRO SEQRES 2 B 204 GLN VAL TYR ASN PHE LYS ARG LEU VAL PHE THR ASN CYS SEQRES 3 B 204 ASN TYR ASN LEU THR LYS LEU LEU SER LEU PHE SER VAL SEQRES 4 B 204 ASN ASP PHE THR CYS SER GLN ILE SER PRO ALA ALA ILE SEQRES 5 B 204 ALA SER ASN CYS TYR SER SER LEU ILE LEU ASP TYR PHE SEQRES 6 B 204 SER TYR PRO LEU SER MET LYS SER ASP LEU SER VAL SER SEQRES 7 B 204 SER ALA GLY PRO ILE SER GLN PHE ASN TYR LYS GLN SER SEQRES 8 B 204 PHE SER ASN PRO THR CYS LEU ILE LEU ALA THR VAL PRO SEQRES 9 B 204 HIS ASN LEU THR THR ILE THR LYS PRO LEU LYS TYR SER SEQRES 10 B 204 TYR ILE ASN LYS CYS SER ARG LEU LEU SER ASP ASP ARG SEQRES 11 B 204 THR GLU VAL PRO GLN LEU VAL ASN ALA ASN GLN TYR SER SEQRES 12 B 204 PRO CYS VAL SER ILE VAL PRO SER THR VAL TRP GLU ASP SEQRES 13 B 204 GLY ASP TYR TYR ARG LYS GLN LEU SER PRO LEU GLU GLY SEQRES 14 B 204 GLY GLY TRP LEU VAL ALA SER GLY SER THR VAL ALA MET SEQRES 15 B 204 THR GLU GLN LEU GLN MET GLY PHE GLY ILE THR VAL GLN SEQRES 16 B 204 TYR GLY THR ASP THR ASN SER VAL CYS MODRES 4L72 ASN A 321 ASN GLYCOSYLATION SITE MODRES 4L72 ASN A 229 ASN GLYCOSYLATION SITE MODRES 4L72 ASN A 520 ASN GLYCOSYLATION SITE MODRES 4L72 ASN A 219 ASN GLYCOSYLATION SITE MODRES 4L72 ASN A 150 ASN GLYCOSYLATION SITE MODRES 4L72 ASN A 85 ASN GLYCOSYLATION SITE MODRES 4L72 ASN A 92 ASN GLYCOSYLATION SITE MODRES 4L72 ASN A 281 ASN GLYCOSYLATION SITE HET NAG C 1 14 HET NAG C 2 14 HET NAG D 1 14 HET NAG D 2 14 HET BMA D 3 11 HET NAG E 1 14 HET NAG E 2 14 HET NAG A 801 14 HET NAG A 802 14 HET NAG A 803 14 HET NAG A 811 14 HET NAG A 812 14 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM BMA BETA-D-MANNOPYRANOSE HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE HETSYN BMA BETA-D-MANNOSE; D-MANNOSE; MANNOSE FORMUL 3 NAG 11(C8 H15 N O6) FORMUL 4 BMA C6 H12 O6 HELIX 1 1 THR A 44 ASN A 51 1 8 HELIX 2 2 LYS A 71 ASN A 75 5 5 HELIX 3 3 GLU A 91 ASP A 96 5 6 HELIX 4 4 ASP A 200 VAL A 207 1 8 HELIX 5 5 PRO A 290 ILE A 295 1 6 HELIX 6 6 GLU A 421 MET A 425 5 5 HELIX 7 7 ASN A 497 ASN A 506 1 10 HELIX 8 8 ASN A 562 ASN A 572 1 11 HELIX 9 9 GLY A 587 HIS A 592 1 6 HELIX 10 10 ALA A 593 ASN A 595 5 3 HELIX 11 11 THR A 600 MET A 616 1 17 HELIX 12 12 SER A 630 GLY A 641 1 12 HELIX 13 13 ASP A 663 GLY A 672 1 10 HELIX 14 14 ASN A 679 SER A 686 1 8 HELIX 15 15 THR A 687 VAL A 698 5 12 HELIX 16 16 HIS A 712 VAL A 726 1 15 HELIX 17 17 SER A 744 PHE A 763 1 20 HELIX 18 18 GLN B 395 PHE B 399 5 5 HELIX 19 19 SER B 429 ASN B 436 1 8 HELIX 20 20 PRO B 449 LEU B 456 5 8 HELIX 21 21 GLY B 462 ASN B 468 1 7 SHEET 1 A 2 LYS A 41 THR A 42 0 SHEET 2 A 2 VAL A 507 GLN A 508 1 O GLN A 508 N LYS A 41 SHEET 1 B 4 ARG A 61 TRP A 62 0 SHEET 2 B 4 GLU A 67 TYR A 70 -1 O LEU A 69 N ARG A 61 SHEET 3 B 4 ILE A 76 ASN A 80 -1 O LEU A 77 N TYR A 70 SHEET 4 B 4 SER A 86 LEU A 90 -1 O LEU A 90 N ILE A 76 SHEET 1 C 4 ILE A 102 ILE A 107 0 SHEET 2 C 4 PHE A 113 LYS A 122 -1 O GLU A 117 N ASP A 104 SHEET 3 C 4 TYR A 128 ASP A 136 -1 O ASP A 133 N LEU A 116 SHEET 4 C 4 GLN A 141 LEU A 142 -1 O GLN A 141 N ASP A 136 SHEET 1 D 4 TRP A 154 TRP A 157 0 SHEET 2 D 4 LEU A 164 TRP A 168 -1 O ALA A 165 N THR A 156 SHEET 3 D 4 ASP A 171 LYS A 175 -1 O TYR A 173 N TYR A 166 SHEET 4 D 4 TYR A 183 ARG A 184 -1 O TYR A 183 N VAL A 174 SHEET 1 E 3 ILE A 194 ASN A 196 0 SHEET 2 E 3 PHE A 222 ASN A 229 -1 O PHE A 228 N TYR A 195 SHEET 3 E 3 LEU A 214 TRP A 216 -1 N TRP A 215 O ALA A 224 SHEET 1 F 4 ILE A 194 ASN A 196 0 SHEET 2 F 4 PHE A 222 ASN A 229 -1 O PHE A 228 N TYR A 195 SHEET 3 F 4 THR A 265 ASN A 272 -1 O PHE A 269 N TYR A 225 SHEET 4 F 4 SER A 284 ILE A 287 -1 O ILE A 285 N VAL A 270 SHEET 1 G 2 LEU A 235 PHE A 240 0 SHEET 2 G 2 LYS A 250 PRO A 255 -1 O LYS A 250 N PHE A 240 SHEET 1 H 4 HIS A 298 THR A 307 0 SHEET 2 H 4 ARG A 310 ARG A 317 -1 O SER A 312 N THR A 304 SHEET 3 H 4 TYR A 322 TYR A 330 -1 O TYR A 322 N ARG A 317 SHEET 4 H 4 TRP A 337 ASN A 338 -1 O ASN A 338 N ASP A 329 SHEET 1 I 4 HIS A 298 THR A 307 0 SHEET 2 I 4 ARG A 310 ARG A 317 -1 O SER A 312 N THR A 304 SHEET 3 I 4 TYR A 322 TYR A 330 -1 O TYR A 322 N ARG A 317 SHEET 4 I 4 HIS A 345 MET A 348 -1 O GLU A 347 N SER A 323 SHEET 1 J 4 HIS A 363 PHE A 364 0 SHEET 2 J 4 SER A 370 SER A 376 -1 O TYR A 372 N HIS A 363 SHEET 3 J 4 ARG A 382 GLN A 388 -1 O PHE A 387 N PHE A 371 SHEET 4 J 4 LYS A 391 PHE A 396 -1 O THR A 395 N TYR A 386 SHEET 1 K 4 VAL A 404 LEU A 410 0 SHEET 2 K 4 TYR A 414 SER A 419 -1 O TYR A 416 N ALA A 409 SHEET 3 K 4 ASN A 430 GLN A 435 -1 O TYR A 432 N TYR A 417 SHEET 4 K 4 ASP A 438 CYS A 444 -1 O THR A 443 N LYS A 433 SHEET 1 L 4 TYR A 457 PHE A 461 0 SHEET 2 L 4 TYR A 467 CYS A 472 -1 O ARG A 471 N SER A 458 SHEET 3 L 4 LEU A 479 SER A 484 -1 O HIS A 483 N TYR A 468 SHEET 4 L 4 ARG A 492 GLU A 495 -1 O GLU A 495 N TYR A 480 SHEET 1 M 8 SER A 511 LEU A 519 0 SHEET 2 M 8 THR A 522 LEU A 530 -1 O LEU A 530 N SER A 511 SHEET 3 M 8 ILE A 574 PHE A 578 -1 O VAL A 575 N ILE A 529 SHEET 4 M 8 TYR A 540 ASP A 545 1 N ASP A 545 O ALA A 576 SHEET 5 M 8 VAL A 619 TRP A 629 1 O ASP A 620 N TYR A 540 SHEET 6 M 8 CYS A 649 VAL A 653 1 O VAL A 653 N GLY A 628 SHEET 7 M 8 GLU A 699 GLY A 705 1 O LEU A 701 N ALA A 652 SHEET 8 M 8 GLN A 731 TYR A 735 1 O GLN A 731 N TYR A 700 SHEET 1 N 5 LYS B 400 PHE B 404 0 SHEET 2 N 5 SER B 440 SER B 447 -1 O LEU B 441 N PHE B 404 SHEET 3 N 5 GLN B 568 GLN B 576 -1 O GLY B 572 N ASP B 444 SHEET 4 N 5 THR B 477 THR B 483 -1 N ALA B 482 O MET B 569 SHEET 5 N 5 SER B 419 SER B 426 -1 N ASN B 421 O LEU B 481 SHEET 1 O 2 CYS B 407 ASN B 408 0 SHEET 2 O 2 VAL B 584 CYS B 585 1 O CYS B 585 N CYS B 407 SHEET 1 P 4 GLU B 513 PRO B 515 0 SHEET 2 P 4 LYS B 496 LEU B 506 -1 N ARG B 505 O VAL B 514 SHEET 3 P 4 TRP B 553 ALA B 562 -1 O SER B 559 N TYR B 499 SHEET 4 P 4 TYR B 540 GLN B 544 -1 N TYR B 541 O ALA B 556 SSBOND 1 CYS A 328 CYS A 339 1555 1555 2.05 SSBOND 2 CYS A 385 CYS A 394 1555 1555 2.06 SSBOND 3 CYS A 444 CYS A 447 1555 1555 2.04 SSBOND 4 CYS A 454 CYS A 472 1555 1555 2.08 SSBOND 5 CYS A 649 CYS A 762 1555 1555 2.04 SSBOND 6 CYS B 383 CYS B 407 1555 1555 2.04 SSBOND 7 CYS B 425 CYS B 478 1555 1555 2.05 SSBOND 8 CYS B 437 CYS B 585 1555 1555 2.05 SSBOND 9 CYS B 503 CYS B 526 1555 1555 2.05 LINK ND2 ASN A 85 C1 NAG A 801 1555 1555 1.47 LINK ND2 ASN A 92 C1 NAG A 802 1555 1555 1.47 LINK ND2 ASN A 150 C1 NAG A 803 1555 1555 1.46 LINK ND2 ASN A 219 C1 NAG C 1 1555 1555 1.46 LINK ND2 ASN A 229 C1 NAG D 1 1555 1555 1.45 LINK ND2 ASN A 281 C1 NAG E 1 1555 1555 1.47 LINK ND2 ASN A 321 C1 NAG A 811 1555 1555 1.44 LINK ND2 ASN A 520 C1 NAG A 812 1555 1555 1.45 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.46 LINK O4 NAG D 1 C1 NAG D 2 1555 1555 1.44 LINK O4 NAG D 2 C1 BMA D 3 1555 1555 1.46 LINK O4 NAG E 1 C1 NAG E 2 1555 1555 1.45 CISPEP 1 GLY A 474 PRO A 475 0 -0.18 CISPEP 2 PHE B 385 SER B 386 0 13.65 CISPEP 3 GLY B 578 THR B 579 0 -10.79 CRYST1 110.609 110.609 527.713 90.00 90.00 120.00 P 61 2 2 12 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 0.009041 0.005220 0.000000 0.00000 SCALE2 0.000000 0.010439 0.000000 0.00000 SCALE3 0.000000 0.000000 0.001895 0.00000