HEADER VIRAL PROTEIN 08-DEC-17 5YY5 TITLE STRUCTURAL DEFINITION OF A UNIQUE NEUTRALIZATION EPITOPE ON THE TITLE 2 RECEPTOR-BINDING DOMAIN OF MERS-COV SPIKE GLYCOPROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: MERS-COV RBD; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: HEAVY CHAIN; COMPND 7 CHAIN: H; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: LIGHT CHAIN; COMPND 11 CHAIN: L; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 4; COMPND 14 MOLECULE: HEAVY CHAIN; COMPND 15 CHAIN: C; COMPND 16 ENGINEERED: YES; COMPND 17 MOL_ID: 5; COMPND 18 MOLECULE: LIGHT CHAIN; COMPND 19 CHAIN: D; COMPND 20 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MIDDLE EAST RESPIRATORY SYNDROME CORONAVIRUS; SOURCE 3 ORGANISM_TAXID: 1335626; SOURCE 4 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 8 ORGANISM_TAXID: 9606; SOURCE 9 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 11 EXPRESSION_SYSTEM_CELL_LINE: HEK293; SOURCE 12 MOL_ID: 3; SOURCE 13 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 16 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 17 MOL_ID: 4; SOURCE 18 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 19 ORGANISM_TAXID: 9606; SOURCE 20 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 21 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 22 MOL_ID: 5; SOURCE 23 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 24 ORGANISM_TAXID: 9606; SOURCE 25 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 26 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS MERS-COV, SPIKE GLYCORPTOTEIN, NEUTRALIZING ANTIBODY, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.ZHANG,P.WANG,P.ZHOU,X.WANG,L.ZHANG REVDAT 3 29-JUL-20 5YY5 1 COMPND REMARK HETNAM LINK REVDAT 3 2 1 SITE REVDAT 2 20-FEB-19 5YY5 1 AUTHOR JRNL REVDAT 1 01-AUG-18 5YY5 0 JRNL AUTH S.ZHANG,P.ZHOU,P.WANG,Y.LI,L.JIANG,W.JIA,H.WANG,A.FAN, JRNL AUTH 2 D.WANG,X.SHI,X.FANG,M.HAMMEL,S.WANG,X.WANG,L.ZHANG JRNL TITL STRUCTURAL DEFINITION OF A UNIQUE NEUTRALIZATION EPITOPE ON JRNL TITL 2 THE RECEPTOR-BINDING DOMAIN OF MERS-COV SPIKE GLYCOPROTEIN JRNL REF CELL REP V. 24 441 2018 JRNL REFN ESSN 2211-1247 JRNL PMID 29996104 JRNL DOI 10.1016/J.CELREP.2018.06.041 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.11.1_2575: ???) 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) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.51 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.970 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 31541 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.248 REMARK 3 R VALUE (WORKING SET) : 0.246 REMARK 3 FREE R VALUE : 0.279 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1546 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 41.5150 - 6.2208 1.00 2751 127 0.1996 0.2117 REMARK 3 2 6.2208 - 4.9402 1.00 2716 154 0.2243 0.2308 REMARK 3 3 4.9402 - 4.3165 1.00 2736 145 0.2063 0.2116 REMARK 3 4 4.3165 - 3.9222 1.00 2731 136 0.2393 0.2899 REMARK 3 5 3.9222 - 3.6412 1.00 2711 162 0.2523 0.3502 REMARK 3 6 3.6412 - 3.4267 1.00 2692 171 0.2677 0.3214 REMARK 3 7 3.4267 - 3.2551 1.00 2722 136 0.2745 0.3766 REMARK 3 8 3.2551 - 3.1135 1.00 2779 115 0.3198 0.3997 REMARK 3 9 3.1135 - 2.9937 1.00 2738 128 0.3388 0.3708 REMARK 3 10 2.9937 - 2.8904 1.00 2708 145 0.3678 0.4031 REMARK 3 11 2.8904 - 2.8000 0.99 2711 127 0.4239 0.5067 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) : 0.440 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 40.110 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 : 0.009 6764 REMARK 3 ANGLE : 1.332 9231 REMARK 3 CHIRALITY : 0.064 1033 REMARK 3 PLANARITY : 0.008 1178 REMARK 3 DIHEDRAL : 14.412 4001 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 4.1861 42.7230-102.7992 REMARK 3 T TENSOR REMARK 3 T11: 0.8841 T22: 0.9316 REMARK 3 T33: 0.7968 T12: -0.0093 REMARK 3 T13: 0.0481 T23: 0.0323 REMARK 3 L TENSOR REMARK 3 L11: 1.8835 L22: 2.9215 REMARK 3 L33: 0.2657 L12: -0.6660 REMARK 3 L13: -0.0962 L23: -0.1083 REMARK 3 S TENSOR REMARK 3 S11: 0.1502 S12: -0.1943 S13: 0.4555 REMARK 3 S21: -0.0574 S22: -0.1795 S23: -0.4634 REMARK 3 S31: -0.0719 S32: 0.1312 S33: 0.0012 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 5YY5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-DEC-17. REMARK 100 THE DEPOSITION ID IS D_1300006106. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-JUL-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.987 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31541 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 5.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.88 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 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 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: TRIS PH7.5, POLYETHYLENE GLYCOL 8000, REMARK 280 ETHYLENE GLYCOL, VAPOR DIFFUSION, TEMPERATURE 291.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3 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 0.00000 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 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 76.15750 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 43.96955 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 49.51167 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 76.15750 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 43.96955 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 49.51167 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 76.15750 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 43.96955 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 49.51167 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 87.93911 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 99.02333 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 87.93911 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 99.02333 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 87.93911 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 99.02333 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3580 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19200 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, H, L 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3650 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18780 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, C, D REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: 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 ND2 ASN A 410 O5 NAG A 601 2.16 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 506 CA - CB - CG ANGL. DEV. = 18.5 DEGREES REMARK 500 CYS B 425 CA - CB - SG ANGL. DEV. = 7.5 DEGREES REMARK 500 CYS B 437 CA - CB - SG ANGL. DEV. = 7.7 DEGREES REMARK 500 TRP B 535 CA - CB - CG ANGL. DEV. = -14.4 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 PHE A 423 88.21 -150.34 REMARK 500 ARG A 511 -44.48 -134.73 REMARK 500 THR A 579 -79.01 -90.20 REMARK 500 PHE B 423 84.12 -152.35 REMARK 500 SER B 504 -169.45 -121.78 REMARK 500 ARG B 511 -45.70 -140.16 REMARK 500 THR B 579 -77.53 -94.22 REMARK 500 ARG H 16 -159.93 -81.64 REMARK 500 CYS H 22 114.09 -164.24 REMARK 500 SER H 30 19.37 -67.20 REMARK 500 SER H 55 -128.58 -68.27 REMARK 500 ASN H 94 -120.44 -93.25 REMARK 500 VAL H 106 117.58 -163.45 REMARK 500 GLN L 1 129.27 -21.72 REMARK 500 SER L 9 -32.24 -151.04 REMARK 500 ALA L 10 103.59 18.26 REMARK 500 ASN L 28 -83.31 -116.12 REMARK 500 ASN L 52 73.98 29.47 REMARK 500 ASP L 53 -19.19 143.04 REMARK 500 SER L 68 -88.90 -82.83 REMARK 500 SER L 97 55.62 36.82 REMARK 500 SER C 7 -165.53 -161.04 REMARK 500 CYS C 22 118.72 -162.33 REMARK 500 SER C 30 9.89 -65.27 REMARK 500 VAL C 48 -67.40 -108.89 REMARK 500 SER C 55 -139.07 -66.79 REMARK 500 ASN C 82B 60.42 35.57 REMARK 500 ASN C 94 -119.62 -95.41 REMARK 500 PRO D 8 66.67 -105.19 REMARK 500 SER D 9 -34.68 -144.66 REMARK 500 ALA D 10 112.53 22.16 REMARK 500 ASN D 28 -78.17 -119.91 REMARK 500 LEU D 48 -60.91 -99.51 REMARK 500 ASN D 52 69.05 30.31 REMARK 500 ASP D 53 -23.82 146.97 REMARK 500 SER D 68 -88.96 -81.97 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 THR H 93 ASN H 94 148.34 REMARK 500 THR C 93 ASN C 94 149.86 REMARK 500 REMARK 500 REMARK: NULL DBREF 5YY5 A 380 588 PDB 5YY5 5YY5 380 588 DBREF 5YY5 B 380 588 PDB 5YY5 5YY5 380 588 DBREF 5YY5 H 1 96 PDB 5YY5 5YY5 1 96 DBREF 5YY5 L -1 110 PDB 5YY5 5YY5 -1 110 DBREF 5YY5 C 1 105 PDB 5YY5 5YY5 1 105 DBREF 5YY5 D 4 108 PDB 5YY5 5YY5 4 108 SEQRES 1 A 209 GLY VAL GLU CYS ASP PHE SER PRO LEU LEU SER GLY THR SEQRES 2 A 209 PRO PRO GLN VAL TYR ASN PHE LYS ARG LEU VAL PHE THR SEQRES 3 A 209 ASN CYS ASN TYR ASN LEU THR LYS LEU LEU SER LEU PHE SEQRES 4 A 209 SER VAL ASN ASP PHE THR CYS SER GLN ILE SER PRO ALA SEQRES 5 A 209 ALA ILE ALA SER ASN CYS TYR SER SER LEU ILE LEU ASP SEQRES 6 A 209 TYR PHE SER TYR PRO LEU SER MET LYS SER ASP LEU SER SEQRES 7 A 209 VAL SER SER ALA GLY PRO ILE SER GLN PHE ASN TYR LYS SEQRES 8 A 209 GLN SER PHE SER ASN PRO THR CYS LEU ILE LEU ALA THR SEQRES 9 A 209 VAL PRO HIS ASN LEU THR THR ILE THR LYS PRO LEU LYS SEQRES 10 A 209 TYR SER TYR ILE ASN LYS CYS SER ARG LEU LEU SER ASP SEQRES 11 A 209 ASP ARG THR GLU VAL PRO GLN LEU VAL ASN ALA ASN GLN SEQRES 12 A 209 TYR SER PRO CYS VAL SER ILE VAL PRO SER THR VAL TRP SEQRES 13 A 209 GLU ASP GLY ASP TYR TYR ARG LYS GLN LEU SER PRO LEU SEQRES 14 A 209 GLU GLY GLY GLY TRP LEU VAL ALA SER GLY SER THR VAL SEQRES 15 A 209 ALA MET THR GLU GLN LEU GLN MET GLY PHE GLY ILE THR SEQRES 16 A 209 VAL GLN TYR GLY THR ASP THR ASN SER VAL CYS PRO LYS SEQRES 17 A 209 LEU SEQRES 1 B 209 GLY VAL GLU CYS ASP PHE SER PRO LEU LEU SER GLY THR SEQRES 2 B 209 PRO PRO GLN VAL TYR ASN PHE LYS ARG LEU VAL PHE THR SEQRES 3 B 209 ASN CYS ASN TYR ASN LEU THR LYS LEU LEU SER LEU PHE SEQRES 4 B 209 SER VAL ASN ASP PHE THR CYS SER GLN ILE SER PRO ALA SEQRES 5 B 209 ALA ILE ALA SER ASN CYS TYR SER SER LEU ILE LEU ASP SEQRES 6 B 209 TYR PHE SER TYR PRO LEU SER MET LYS SER ASP LEU SER SEQRES 7 B 209 VAL SER SER ALA GLY PRO ILE SER GLN PHE ASN TYR LYS SEQRES 8 B 209 GLN SER PHE SER ASN PRO THR CYS LEU ILE LEU ALA THR SEQRES 9 B 209 VAL PRO HIS ASN LEU THR THR ILE THR LYS PRO LEU LYS SEQRES 10 B 209 TYR SER TYR ILE ASN LYS CYS SER ARG LEU LEU SER ASP SEQRES 11 B 209 ASP ARG THR GLU VAL PRO GLN LEU VAL ASN ALA ASN GLN SEQRES 12 B 209 TYR SER PRO CYS VAL SER ILE VAL PRO SER THR VAL TRP SEQRES 13 B 209 GLU ASP GLY ASP TYR TYR ARG LYS GLN LEU SER PRO LEU SEQRES 14 B 209 GLU GLY GLY GLY TRP LEU VAL ALA SER GLY SER THR VAL SEQRES 15 B 209 ALA MET THR GLU GLN LEU GLN MET GLY PHE GLY ILE THR SEQRES 16 B 209 VAL GLN TYR GLY THR ASP THR ASN SER VAL CYS PRO LYS SEQRES 17 B 209 LEU SEQRES 1 H 111 GLU VAL GLN LEU VAL GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 H 111 PRO GLY ARG SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 H 111 PHE THR PHE SER ASN TYR ALA MET TYR TRP VAL ARG GLN SEQRES 4 H 111 ALA PRO GLY LYS GLY LEU GLU TRP VAL ALA LEU ILE SER SEQRES 5 H 111 TYR ASP ILE SER THR ASP TYR TYR ALA ASP SER VAL LYS SEQRES 6 H 111 GLY ARG PHE THR ILE SER ARG ASP ASN SER LYS ASN THR SEQRES 7 H 111 ILE TYR LEU GLN MET ASN ASN LEU ARG THR GLU ASP THR SEQRES 8 H 111 ALA LEU TYR TYR CYS THR ASN THR TYR TYR TRP GLY GLN SEQRES 9 H 111 GLY THR LEU VAL THR VAL SER SEQRES 1 L 112 GLY SER GLN PRO VAL LEU THR GLN SER PRO SER ALA SER SEQRES 2 L 112 GLY THR PRO GLY GLN ARG VAL THR ILE SER CYS SER GLY SEQRES 3 L 112 SER SER SER ASN ILE GLY ASN ASN TYR VAL TYR TRP TYR SEQRES 4 L 112 GLN GLN LEU PRO GLY THR ALA PRO LYS LEU LEU ILE TYR SEQRES 5 L 112 TRP ASN ASP GLN ARG PRO SER GLY VAL PRO ASP ARG PHE SEQRES 6 L 112 SER GLY SER LYS SER GLY THR SER ALA SER LEU ALA ILE SEQRES 7 L 112 SER GLY LEU ARG SER GLU ASP GLU ALA ASP TYR TYR CYS SEQRES 8 L 112 ALA ALA TRP ASP ASP SER LEU SER GLY ALA VAL PHE GLY SEQRES 9 L 112 GLY GLY THR GLN LEU THR VAL LEU SEQRES 1 C 109 GLY VAL GLN LEU VAL GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 C 109 PRO GLY ARG SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 C 109 PHE THR PHE SER ASN TYR ALA MET TYR TRP VAL ARG GLN SEQRES 4 C 109 ALA PRO GLY LYS GLY LEU GLU TRP VAL ALA LEU ILE SER SEQRES 5 C 109 TYR ASP ILE SER THR ASP TYR TYR ALA ASP SER VAL LYS SEQRES 6 C 109 GLY ARG PHE THR ILE SER ARG ASP ASN SER LYS ASN THR SEQRES 7 C 109 ILE TYR LEU GLN MET ASN ASN LEU ARG THR GLU ASP THR SEQRES 8 C 109 ALA LEU TYR TYR CYS THR ASN THR TYR TYR TRP GLY GLN SEQRES 9 C 109 GLY THR LEU VAL THR SEQRES 1 D 105 LEU THR GLN SER PRO SER ALA SER GLY THR PRO GLY GLN SEQRES 2 D 105 ARG VAL THR ILE SER CYS SER GLY SER SER SER ASN ILE SEQRES 3 D 105 GLY ASN ASN TYR VAL TYR TRP TYR GLN GLN LEU PRO GLY SEQRES 4 D 105 THR ALA PRO LYS LEU LEU ILE TYR TRP ASN ASP GLN ARG SEQRES 5 D 105 PRO SER GLY VAL PRO ASP ARG PHE SER GLY SER LYS SER SEQRES 6 D 105 GLY THR SER ALA SER LEU ALA ILE SER GLY LEU ARG SER SEQRES 7 D 105 GLU ASP GLU ALA ASP TYR TYR CYS ALA ALA TRP ASP ASP SEQRES 8 D 105 SER LEU SER GLY ALA VAL PHE GLY GLY GLY THR GLN LEU SEQRES 9 D 105 THR HET NAG A 601 14 HET NAG B 601 14 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE FORMUL 7 NAG 2(C8 H15 N O6) HELIX 1 AA1 PHE A 385 SER A 390 5 6 HELIX 2 AA2 GLN A 395 PHE A 399 5 5 HELIX 3 AA3 ASN A 410 LEU A 417 1 8 HELIX 4 AA4 SER A 429 ALA A 434 1 6 HELIX 5 AA5 PRO A 449 LEU A 456 5 8 HELIX 6 AA6 GLY A 462 ASN A 468 1 7 HELIX 7 AA7 SER A 524 SER A 528 5 5 HELIX 8 AA8 SER A 546 GLY A 550 5 5 HELIX 9 AA9 PHE B 385 SER B 390 5 6 HELIX 10 AB1 GLN B 395 PHE B 399 5 5 HELIX 11 AB2 ASN B 410 LEU B 417 1 8 HELIX 12 AB3 SER B 429 ALA B 434 1 6 HELIX 13 AB4 PRO B 449 LEU B 456 5 8 HELIX 14 AB5 GLY B 462 ASN B 468 1 7 HELIX 15 AB6 SER B 524 SER B 528 5 5 HELIX 16 AB7 SER B 546 GLY B 550 5 5 HELIX 17 AB8 THR H 28 TYR H 32 5 5 HELIX 18 AB9 ARG H 83 THR H 87 5 5 HELIX 19 AC1 THR C 28 TYR C 32 5 5 SHEET 1 AA1 5 LYS A 400 PHE A 404 0 SHEET 2 AA1 5 SER A 440 SER A 447 -1 O LEU A 441 N PHE A 404 SHEET 3 AA1 5 GLN A 568 GLN A 576 -1 O GLY A 572 N ASP A 444 SHEET 4 AA1 5 THR A 477 THR A 483 -1 N ILE A 480 O PHE A 571 SHEET 5 AA1 5 ASP A 422 SER A 426 -1 N ASP A 422 O LEU A 481 SHEET 1 AA2 2 CYS A 407 TYR A 409 0 SHEET 2 AA2 2 VAL A 584 PRO A 586 1 O CYS A 585 N CYS A 407 SHEET 1 AA3 3 LYS A 496 LEU A 506 0 SHEET 2 AA3 3 TRP A 553 ALA A 562 -1 O VAL A 561 N TYR A 497 SHEET 3 AA3 3 TYR A 540 GLN A 544 -1 N TYR A 541 O ALA A 556 SHEET 1 AA4 5 LYS B 400 PHE B 404 0 SHEET 2 AA4 5 SER B 440 SER B 447 -1 O LEU B 443 N LEU B 402 SHEET 3 AA4 5 GLN B 568 GLN B 576 -1 O GLY B 572 N ASP B 444 SHEET 4 AA4 5 THR B 477 THR B 483 -1 N ILE B 480 O PHE B 571 SHEET 5 AA4 5 SER B 419 SER B 426 -1 N ASN B 421 O LEU B 481 SHEET 1 AA5 2 CYS B 407 TYR B 409 0 SHEET 2 AA5 2 VAL B 584 PRO B 586 1 O CYS B 585 N CYS B 407 SHEET 1 AA6 4 GLU B 513 PRO B 515 0 SHEET 2 AA6 4 TYR B 497 LEU B 506 -1 N ARG B 505 O VAL B 514 SHEET 3 AA6 4 TRP B 553 VAL B 561 -1 O SER B 557 N LYS B 502 SHEET 4 AA6 4 TYR B 540 GLN B 544 -1 N TYR B 541 O ALA B 556 SHEET 1 AA7 4 GLN H 3 SER H 7 0 SHEET 2 AA7 4 SER H 17 SER H 25 -1 O ALA H 23 N VAL H 5 SHEET 3 AA7 4 THR H 77 ASN H 82A-1 O LEU H 80 N LEU H 20 SHEET 4 AA7 4 THR H 68 ASP H 72 -1 N THR H 68 O GLN H 81 SHEET 1 AA8 6 GLY H 10 VAL H 12 0 SHEET 2 AA8 6 LEU H 103 VAL H 106 1 O THR H 105 N GLY H 10 SHEET 3 AA8 6 ALA H 88 THR H 93 -1 N ALA H 88 O VAL H 104 SHEET 4 AA8 6 MET H 34 GLN H 39 -1 N VAL H 37 O TYR H 91 SHEET 5 AA8 6 LEU H 45 ILE H 51 -1 O ILE H 51 N MET H 34 SHEET 6 AA8 6 ASP H 57 TYR H 59 -1 O TYR H 58 N LEU H 50 SHEET 1 AA9 4 THR L 5 GLN L 6 0 SHEET 2 AA9 4 VAL L 18 SER L 23 -1 O SER L 23 N THR L 5 SHEET 3 AA9 4 SER L 71 ILE L 76 -1 O ALA L 72 N CYS L 22 SHEET 4 AA9 4 PHE L 63 LYS L 67 -1 N SER L 66 O SER L 73 SHEET 1 AB1 2 SER L 11 GLY L 12 0 SHEET 2 AB1 2 THR L 108 VAL L 109 1 O THR L 108 N GLY L 12 SHEET 1 AB2 4 LYS L 46 ILE L 49 0 SHEET 2 AB2 4 TYR L 35 GLN L 39 -1 N TRP L 36 O ILE L 49 SHEET 3 AB2 4 ASP L 86 ASP L 93 -1 O ASP L 86 N GLN L 39 SHEET 4 AB2 4 GLY L 98 PHE L 101 -1 O VAL L 100 N ALA L 91 SHEET 1 AB3 4 LYS L 46 ILE L 49 0 SHEET 2 AB3 4 TYR L 35 GLN L 39 -1 N TRP L 36 O ILE L 49 SHEET 3 AB3 4 ASP L 86 ASP L 93 -1 O ASP L 86 N GLN L 39 SHEET 4 AB3 4 THR L 105 GLN L 106 -1 O THR L 105 N TYR L 87 SHEET 1 AB4 4 GLN C 3 GLU C 6 0 SHEET 2 AB4 4 LEU C 18 SER C 25 -1 O SER C 25 N GLN C 3 SHEET 3 AB4 4 THR C 77 MET C 82 -1 O LEU C 80 N LEU C 20 SHEET 4 AB4 4 PHE C 67 ASP C 72 -1 N THR C 68 O GLN C 81 SHEET 1 AB5 5 ASP C 57 TYR C 59 0 SHEET 2 AB5 5 LEU C 45 ILE C 51 -1 N LEU C 50 O TYR C 58 SHEET 3 AB5 5 MET C 34 GLN C 39 -1 N ARG C 38 O GLU C 46 SHEET 4 AB5 5 ALA C 88 THR C 93 -1 O TYR C 91 N VAL C 37 SHEET 5 AB5 5 THR C 102 VAL C 104 -1 O THR C 102 N TYR C 90 SHEET 1 AB6 4 THR D 5 GLN D 6 0 SHEET 2 AB6 4 VAL D 18 SER D 23 -1 O SER D 23 N THR D 5 SHEET 3 AB6 4 SER D 71 ILE D 76 -1 O ALA D 72 N CYS D 22 SHEET 4 AB6 4 PHE D 63 LYS D 67 -1 N SER D 66 O SER D 73 SHEET 1 AB7 4 LYS D 46 ILE D 49 0 SHEET 2 AB7 4 VAL D 34 GLN D 39 -1 N TRP D 36 O ILE D 49 SHEET 3 AB7 4 ASP D 86 ASP D 93 -1 O ASP D 86 N GLN D 39 SHEET 4 AB7 4 GLY D 98 PHE D 101 -1 O VAL D 100 N ALA D 91 SHEET 1 AB8 4 LYS D 46 ILE D 49 0 SHEET 2 AB8 4 VAL D 34 GLN D 39 -1 N TRP D 36 O ILE D 49 SHEET 3 AB8 4 ASP D 86 ASP D 93 -1 O ASP D 86 N GLN D 39 SHEET 4 AB8 4 THR D 105 GLN D 106 -1 O THR D 105 N TYR D 87 SSBOND 1 CYS A 383 CYS A 407 1555 1555 1.99 SSBOND 2 CYS A 425 CYS A 478 1555 1555 2.00 SSBOND 3 CYS A 437 CYS A 585 1555 1555 2.00 SSBOND 4 CYS A 503 CYS A 526 1555 1555 2.01 SSBOND 5 CYS B 383 CYS B 407 1555 1555 1.97 SSBOND 6 CYS B 425 CYS B 478 1555 1555 2.02 SSBOND 7 CYS B 437 CYS B 585 1555 1555 2.05 SSBOND 8 CYS B 503 CYS B 526 1555 1555 2.03 SSBOND 9 CYS H 22 CYS H 92 1555 1555 2.05 SSBOND 10 CYS L 22 CYS L 89 1555 1555 2.04 SSBOND 11 CYS C 22 CYS C 92 1555 1555 2.03 SSBOND 12 CYS D 22 CYS D 89 1555 1555 2.05 LINK ND2 ASN A 410 C1 NAG A 601 1555 1555 1.46 LINK ND2 ASN B 410 C1 NAG B 601 1555 1555 1.45 LINK CE LYS B 413 O6 NAG B 601 1555 1555 1.38 CRYST1 152.315 152.315 148.535 90.00 90.00 120.00 H 3 18 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 0.006565 0.003791 0.000000 0.00000 SCALE2 0.000000 0.007581 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006732 0.00000