HEADER VIRAL PROTEIN 03-DEC-15 5F4P
TITLE HIV-1 GP120 COMPLEX WITH BNM-III-170
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: ENVELOPE GLYCOPROTEIN GP120 OF HIV-1 CLADE C;
COMPND 3 CHAIN: D, A;
COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1;
SOURCE 3 ORGANISM_TAXID: 11676;
SOURCE 4 EXPRESSION_SYSTEM: HOMO SAPIENS;
SOURCE 5 EXPRESSION_SYSTEM_TAXID: 9606;
SOURCE 6 EXPRESSION_SYSTEM_CELL_LINE: HEK 293 GNTI- CELLS
KEYWDS VIRAL PROTEIN
EXPDTA X-RAY DIFFRACTION
AUTHOR S.LIANG,W.A.HENDRICKSON
REVDAT 4 13-NOV-24 5F4P 1 REMARK
REVDAT 3 27-SEP-23 5F4P 1 HETSYN
REVDAT 2 29-JUL-20 5F4P 1 COMPND REMARK HETNAM SITE
REVDAT 1 30-MAR-16 5F4P 0
JRNL AUTH B.MELILLO,S.LIANG,J.PARK,A.SCHON,J.R.COURTER,J.M.LALONDE,
JRNL AUTH 2 D.J.WENDLER,A.M.PRINCIOTTO,M.S.SEAMAN,E.FREIRE,J.SODROSKI,
JRNL AUTH 3 N.MADANI,W.A.HENDRICKSON,A.B.SMITH
JRNL TITL SMALL-MOLECULE CD4-MIMICS: STRUCTURE-BASED OPTIMIZATION OF
JRNL TITL 2 HIV-1 ENTRY INHIBITION.
JRNL REF ACS MED.CHEM.LETT. V. 7 330 2016
JRNL REFN ISSN 1948-5875
JRNL PMID 26985324
JRNL DOI 10.1021/ACSMEDCHEMLETT.5B00471
REMARK 2
REMARK 2 RESOLUTION. 2.60 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX 1.8.4_1496
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) : 2.60
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.24
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4
REMARK 3 NUMBER OF REFLECTIONS : 25857
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.275
REMARK 3 R VALUE (WORKING SET) : 0.274
REMARK 3 FREE R VALUE : 0.311
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.850
REMARK 3 FREE R VALUE TEST SET COUNT : 1255
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 48.2445 - 5.4061 0.99 2880 150 0.2351 0.2421
REMARK 3 2 5.4061 - 4.2918 0.99 2775 119 0.2328 0.2665
REMARK 3 3 4.2918 - 3.7495 1.00 2736 139 0.2672 0.3194
REMARK 3 4 3.7495 - 3.4068 1.00 2719 166 0.2847 0.3521
REMARK 3 5 3.4068 - 3.1627 1.00 2698 162 0.3263 0.3765
REMARK 3 6 3.1627 - 2.9762 1.00 2705 150 0.3401 0.4031
REMARK 3 7 2.9762 - 2.8272 0.99 2706 133 0.3703 0.4222
REMARK 3 8 2.8272 - 2.7041 0.99 2704 108 0.3689 0.4639
REMARK 3 9 2.7041 - 2.6000 0.99 2679 128 0.3676 0.3388
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) : 0.360
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 36.380
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 : 0.006 5612
REMARK 3 ANGLE : 1.064 7600
REMARK 3 CHIRALITY : 0.047 866
REMARK 3 PLANARITY : 0.006 968
REMARK 3 DIHEDRAL : 15.276 2056
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 5F4P COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-DEC-15.
REMARK 100 THE DEPOSITION ID IS D_1000216009.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 17-APR-15
REMARK 200 TEMPERATURE (KELVIN) : 180
REMARK 200 PH : NULL
REMARK 200 NUMBER OF CRYSTALS USED : NULL
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : APS
REMARK 200 BEAMLINE : 24-ID-C
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : PIXEL
REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : AIMLESS
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26041
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500
REMARK 200 RESOLUTION RANGE LOW (A) : 48.236
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2
REMARK 200 DATA REDUNDANCY : 6.290
REMARK 200 R MERGE (I) : 0.09200
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.1000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL
REMARK 200 COMPLETENESS FOR SHELL (%) : NULL
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: PHASER
REMARK 200 STARTING MODEL: 3TGR
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 54.02
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.68
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 1500, CALCIUM MAGNESIUM CHLORIDE,
REMARK 280 IMIDAZOLE, EVAPORATION, TEMPERATURE 290K
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 96.47250
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 96.47250
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 33.68900
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 63.75850
REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 33.68900
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 63.75850
REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 96.47250
REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 33.68900
REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 63.75850
REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 96.47250
REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 33.68900
REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 63.75850
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: 4000 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 31320 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 46.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, A
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 603 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 ASN D 317
REMARK 465 GLY D 318
REMARK 465 GLY D 319
REMARK 465 SER D 320
REMARK 465 GLY D 321
REMARK 465 SER D 322
REMARK 465 GLY D 323
REMARK 465 GLY D 324
REMARK 465 GLY D 458
REMARK 465 GLY D 459
REMARK 465 ASN D 460
REMARK 465 ASP D 461
REMARK 465 ASP D 462
REMARK 465 ASN D 463
REMARK 465 ILE D 491
REMARK 465 ASN A 317
REMARK 465 GLY A 318
REMARK 465 GLY A 319
REMARK 465 SER A 320
REMARK 465 GLY A 321
REMARK 465 SER A 322
REMARK 465 GLY A 323
REMARK 465 GLY A 324
REMARK 465 GLY A 458
REMARK 465 GLY A 459
REMARK 465 ASN A 460
REMARK 465 ASP A 461
REMARK 465 ASP A 462
REMARK 465 ASN A 463
REMARK 465 ILE A 491
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 O GLU D 268 ND2 ASN D 289 2.09
REMARK 500 OD1 ASN A 340 NZ LYS A 344 2.17
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 PRO D 79 C - N - CA ANGL. DEV. = 9.7 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 CYS D 74 -168.45 -114.10
REMARK 500 PRO D 79 25.72 -44.18
REMARK 500 ASN D 80 70.46 -116.03
REMARK 500 MET D 84 97.82 -55.28
REMARK 500 ALA D 87 29.09 -140.53
REMARK 500 VAL D 89 -92.88 -136.50
REMARK 500 THR D 90 79.94 50.97
REMARK 500 ASN D 98 118.01 -161.86
REMARK 500 SER D 115 -77.28 -104.89
REMARK 500 CYS D 205 63.46 -119.75
REMARK 500 ASP D 211 115.98 -164.35
REMARK 500 PRO D 220 -161.99 -69.44
REMARK 500 LEU D 226 169.75 -48.61
REMARK 500 ARG D 240 -48.24 -130.38
REMARK 500 ASN D 241 92.79 -62.99
REMARK 500 SER D 243 -165.99 -100.95
REMARK 500 GLN D 258 -60.80 62.70
REMARK 500 GLU D 268 -87.80 -113.93
REMARK 500 ILE D 270 127.22 -28.96
REMARK 500 ASN D 289 -55.85 -129.62
REMARK 500 SER D 356 26.64 -153.32
REMARK 500 SER D 365 -75.07 -54.20
REMARK 500 LEU D 390 -75.70 -127.39
REMARK 500 ASN D 392 106.76 -162.12
REMARK 500 ASN D 397 2.18 59.11
REMARK 500 ASN D 411 10.63 55.10
REMARK 500 LYS D 485 -155.40 117.67
REMARK 500 TYR D 486 -140.00 -174.13
REMARK 500 LYS D 487 120.41 177.02
REMARK 500 PRO A 81 79.01 -116.21
REMARK 500 GLU A 83 93.12 -24.76
REMARK 500 VAL A 89 -64.84 -129.22
REMARK 500 THR A 90 94.28 32.02
REMARK 500 ASN A 94 89.06 -153.30
REMARK 500 SER A 115 -77.46 -101.20
REMARK 500 ASP A 211 106.40 -163.23
REMARK 500 PRO A 220 -160.99 -65.49
REMARK 500 THR A 232 13.35 -67.06
REMARK 500 PRO A 253 65.95 -65.40
REMARK 500 GLN A 258 -55.56 63.78
REMARK 500 GLU A 268 -86.92 -134.39
REMARK 500 ASN A 289 -56.14 -127.00
REMARK 500 PRO A 354 -87.20 -34.45
REMARK 500 SER A 365 -80.86 -5.53
REMARK 500 HIS A 374 91.65 -69.55
REMARK 500 LEU A 390 -63.22 -108.48
REMARK 500 ASN A 392 105.87 -168.37
REMARK 500 LEU A 483 44.58 -103.97
REMARK 500 LYS A 485 -145.19 120.22
REMARK 500 TYR A 486 -148.64 176.08
REMARK 500
REMARK 500 THIS ENTRY HAS 51 RAMACHANDRAN OUTLIERS.
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 PHE D 353 PRO D 354 -147.87
REMARK 500 TYR D 484 LYS D 485 128.43
REMARK 500 LYS D 485 TYR D 486 -139.48
REMARK 500 TYR D 486 LYS D 487 135.28
REMARK 500 GLU A 275 ASN A 276 140.78
REMARK 500 TYR A 484 LYS A 485 119.61
REMARK 500 LYS A 485 TYR A 486 -146.10
REMARK 500
REMARK 500 REMARK: NULL
REMARK 610
REMARK 610 MISSING HETEROATOM
REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;
REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 610 I=INSERTION CODE):
REMARK 610 M RES C SSEQI
REMARK 610 NAG D 501
REMARK 610 NAG D 502
REMARK 610 NAG D 503
REMARK 610 NAG D 504
REMARK 610 NAG D 505
REMARK 610 NAG D 506
REMARK 610 NAG A 502
REMARK 610 NAG A 503
REMARK 610 NAG A 504
REMARK 610 NAG A 505
REMARK 610 NAG A 506
REMARK 610 NAG A 507
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 5F4L RELATED DB: PDB
REMARK 900 RELATED ID: 5F4R RELATED DB: PDB
REMARK 900 RELATED ID: 5F4U RELATED DB: PDB
DBREF 5F4P D 49 491 PDB 5F4P 5F4P 49 491
DBREF 5F4P A 49 491 PDB 5F4P 5F4P 49 491
SEQRES 1 D 350 LYS THR THR LEU PHE CYS ALA SER ASP ALA LYS ALA TYR
SEQRES 2 D 350 GLU LYS GLU VAL HIS ASN VAL TRP ALA THR HIS ALA CYS
SEQRES 3 D 350 VAL PRO THR ASP PRO ASN PRO GLN GLU MET VAL LEU ALA
SEQRES 4 D 350 ASN VAL THR GLU ASN PHE ASN MET TRP LYS ASN ASP MET
SEQRES 5 D 350 VAL GLU GLN MET HIS GLU ASP ILE ILE SER LEU TRP ASP
SEQRES 6 D 350 GLU SER LEU LYS PRO CYS VAL LYS LEU THR GLY GLY SER
SEQRES 7 D 350 ALA ILE THR GLN ALA CYS PRO LYS VAL SER PHE ASP PRO
SEQRES 8 D 350 ILE PRO LEU HIS TYR CYS ALA PRO ALA GLY PHE ALA ILE
SEQRES 9 D 350 LEU LYS CYS ASN ASN LYS THR PHE ASN GLY THR GLY PRO
SEQRES 10 D 350 CYS ARG ASN VAL SER THR VAL GLN CYS THR HIS GLY ILE
SEQRES 11 D 350 LYS PRO VAL VAL SER THR GLN LEU LEU LEU ASN GLY SER
SEQRES 12 D 350 LEU ALA GLU GLU GLU ILE ILE ILE ARG SER GLU ASN LEU
SEQRES 13 D 350 THR ASN ASN ALA LYS THR ILE ILE VAL HIS LEU ASN GLU
SEQRES 14 D 350 SER VAL ASN ILE VAL CYS THR ARG PRO ASN ASN GLY GLY
SEQRES 15 D 350 SER GLY SER GLY GLY ASN ILE ARG GLN ALA HIS CYS ASN
SEQRES 16 D 350 ILE ASN GLU SER LYS TRP ASN ASN THR LEU GLN LYS VAL
SEQRES 17 D 350 GLY GLU GLU LEU ALA LYS HIS PHE PRO SER LYS THR ILE
SEQRES 18 D 350 LYS PHE GLU PRO SER SER GLY GLY ASP LEU GLU ILE THR
SEQRES 19 D 350 THR HIS SER PHE ASN CYS ARG GLY GLU PHE PHE TYR CYS
SEQRES 20 D 350 ASN THR SER ASP LEU PHE ASN GLY THR TYR ARG ASN GLY
SEQRES 21 D 350 THR TYR ASN HIS THR GLY ARG SER SER ASN GLY THR ILE
SEQRES 22 D 350 THR LEU GLN CYS LYS ILE LYS GLN ILE ILE ASN MET TRP
SEQRES 23 D 350 GLN GLU VAL GLY ARG ALA ILE TYR ALA PRO PRO ILE GLU
SEQRES 24 D 350 GLY GLU ILE THR CYS ASN SER ASN ILE THR GLY LEU LEU
SEQRES 25 D 350 LEU LEU ARG ASP GLY GLY ASN ASP ASP ASN ASP THR GLU
SEQRES 26 D 350 THR PHE ARG PRO GLY GLY GLY ASP MET ARG ASP ASN TRP
SEQRES 27 D 350 ARG SER GLU LEU TYR LYS TYR LYS VAL VAL GLU ILE
SEQRES 1 A 350 LYS THR THR LEU PHE CYS ALA SER ASP ALA LYS ALA TYR
SEQRES 2 A 350 GLU LYS GLU VAL HIS ASN VAL TRP ALA THR HIS ALA CYS
SEQRES 3 A 350 VAL PRO THR ASP PRO ASN PRO GLN GLU MET VAL LEU ALA
SEQRES 4 A 350 ASN VAL THR GLU ASN PHE ASN MET TRP LYS ASN ASP MET
SEQRES 5 A 350 VAL GLU GLN MET HIS GLU ASP ILE ILE SER LEU TRP ASP
SEQRES 6 A 350 GLU SER LEU LYS PRO CYS VAL LYS LEU THR GLY GLY SER
SEQRES 7 A 350 ALA ILE THR GLN ALA CYS PRO LYS VAL SER PHE ASP PRO
SEQRES 8 A 350 ILE PRO LEU HIS TYR CYS ALA PRO ALA GLY PHE ALA ILE
SEQRES 9 A 350 LEU LYS CYS ASN ASN LYS THR PHE ASN GLY THR GLY PRO
SEQRES 10 A 350 CYS ARG ASN VAL SER THR VAL GLN CYS THR HIS GLY ILE
SEQRES 11 A 350 LYS PRO VAL VAL SER THR GLN LEU LEU LEU ASN GLY SER
SEQRES 12 A 350 LEU ALA GLU GLU GLU ILE ILE ILE ARG SER GLU ASN LEU
SEQRES 13 A 350 THR ASN ASN ALA LYS THR ILE ILE VAL HIS LEU ASN GLU
SEQRES 14 A 350 SER VAL ASN ILE VAL CYS THR ARG PRO ASN ASN GLY GLY
SEQRES 15 A 350 SER GLY SER GLY GLY ASN ILE ARG GLN ALA HIS CYS ASN
SEQRES 16 A 350 ILE ASN GLU SER LYS TRP ASN ASN THR LEU GLN LYS VAL
SEQRES 17 A 350 GLY GLU GLU LEU ALA LYS HIS PHE PRO SER LYS THR ILE
SEQRES 18 A 350 LYS PHE GLU PRO SER SER GLY GLY ASP LEU GLU ILE THR
SEQRES 19 A 350 THR HIS SER PHE ASN CYS ARG GLY GLU PHE PHE TYR CYS
SEQRES 20 A 350 ASN THR SER ASP LEU PHE ASN GLY THR TYR ARG ASN GLY
SEQRES 21 A 350 THR TYR ASN HIS THR GLY ARG SER SER ASN GLY THR ILE
SEQRES 22 A 350 THR LEU GLN CYS LYS ILE LYS GLN ILE ILE ASN MET TRP
SEQRES 23 A 350 GLN GLU VAL GLY ARG ALA ILE TYR ALA PRO PRO ILE GLU
SEQRES 24 A 350 GLY GLU ILE THR CYS ASN SER ASN ILE THR GLY LEU LEU
SEQRES 25 A 350 LEU LEU ARG ASP GLY GLY ASN ASP ASP ASN ASP THR GLU
SEQRES 26 A 350 THR PHE ARG PRO GLY GLY GLY ASP MET ARG ASP ASN TRP
SEQRES 27 A 350 ARG SER GLU LEU TYR LYS TYR LYS VAL VAL GLU ILE
HET NAG D 501 14
HET NAG D 502 14
HET NAG D 503 14
HET NAG D 504 14
HET NAG D 505 14
HET NAG D 506 14
HET 5VG D 507 31
HET 5VG A 501 31
HET NAG A 502 14
HET NAG A 503 14
HET NAG A 504 14
HET NAG A 505 14
HET NAG A 506 14
HET NAG A 507 14
HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE
HETNAM 5VG ~{N}'-[(1~{R},2~{R})-2-(CARBAMIMIDAMIDOMETHYL)-5-
HETNAM 2 5VG (METHYLAMINOMETHYL)-2,3-DIHYDRO-1~{H}-INDEN-1-YL]-
HETNAM 3 5VG ~{N}-(4-CHLORANYL-3-FLUORANYL-PHENYL)ETHANEDIAMIDE
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
FORMUL 3 NAG 12(C8 H15 N O6)
FORMUL 9 5VG 2(C21 H24 CL F N6 O2)
FORMUL 17 HOH *13(H2 O)
HELIX 1 AA1 GLU D 64 CYS D 74 1 11
HELIX 2 AA2 ASN D 98 LEU D 116 1 19
HELIX 3 AA3 GLU D 335 HIS D 352 1 18
HELIX 4 AA4 ASP D 368 THR D 373 1 6
HELIX 5 AA5 ASP D 474 SER D 481 1 8
HELIX 6 AA6 GLU A 64 CYS A 74 1 11
HELIX 7 AA7 ASN A 98 LEU A 116 1 19
HELIX 8 AA8 GLU A 335 PHE A 353 1 19
HELIX 9 AA9 ASP A 368 THR A 373 1 6
HELIX 10 AB1 MET A 475 SER A 481 1 7
SHEET 1 AA1 3 VAL D 75 PRO D 76 0
SHEET 2 AA1 3 PHE D 53 SER D 56 1 N SER D 56 O VAL D 75
SHEET 3 AA1 3 HIS D 216 CYS D 218 -1 O HIS D 216 N ALA D 55
SHEET 1 AA2 2 GLU D 91 ASN D 94 0
SHEET 2 AA2 2 THR D 236 CYS D 239 -1 O CYS D 239 N GLU D 91
SHEET 1 AA3 4 SER D 199 THR D 202 0
SHEET 2 AA3 4 VAL D 120 THR D 123 -1 N THR D 123 O SER D 199
SHEET 3 AA3 4 ARG D 432 ILE D 434 -1 O ARG D 432 N LEU D 122
SHEET 4 AA3 4 ILE D 423 ASN D 425 -1 N ILE D 424 O ALA D 433
SHEET 1 AA4 3 VAL D 242 VAL D 245 0
SHEET 2 AA4 3 ALA D 224 CYS D 228 -1 N ILE D 225 O VAL D 245
SHEET 3 AA4 3 LYS D 487 VAL D 489 -1 O VAL D 489 N ALA D 224
SHEET 1 AA5 7 LEU D 259 LEU D 261 0
SHEET 2 AA5 7 ILE D 443 ARG D 456 -1 O THR D 450 N LEU D 260
SHEET 3 AA5 7 ILE D 284 ARG D 298 -1 N ILE D 284 O LEU D 454
SHEET 4 AA5 7 GLN D 328 ASN D 334 -1 O HIS D 330 N THR D 297
SHEET 5 AA5 7 THR D 413 LYS D 421 -1 O ILE D 414 N ILE D 333
SHEET 6 AA5 7 GLU D 381 CYS D 385 -1 N TYR D 384 O LYS D 419
SHEET 7 AA5 7 HIS D 374 CYS D 378 -1 N CYS D 378 O GLU D 381
SHEET 1 AA6 7 ILE D 271 ARG D 273 0
SHEET 2 AA6 7 ILE D 284 ARG D 298 -1 O HIS D 287 N ILE D 271
SHEET 3 AA6 7 ILE D 443 ARG D 456 -1 O LEU D 454 N ILE D 284
SHEET 4 AA6 7 THR D 465 PRO D 470 -1 O ARG D 469 N LEU D 455
SHEET 5 AA6 7 THR D 358 PHE D 361 1 N THR D 358 O GLU D 466
SHEET 6 AA6 7 GLY D 393 ARG D 396 -1 O GLY D 393 N PHE D 361
SHEET 7 AA6 7 THR D 399 HIS D 405 -1 O ASN D 404 N THR D 394
SHEET 1 AA7 3 VAL A 75 PRO A 76 0
SHEET 2 AA7 3 PHE A 53 SER A 56 1 N SER A 56 O VAL A 75
SHEET 3 AA7 3 HIS A 216 CYS A 218 -1 O CYS A 218 N PHE A 53
SHEET 1 AA8 2 GLU A 91 ASN A 94 0
SHEET 2 AA8 2 THR A 236 CYS A 239 -1 O GLY A 237 N PHE A 93
SHEET 1 AA9 4 SER A 199 THR A 202 0
SHEET 2 AA9 4 VAL A 120 THR A 123 -1 N THR A 123 O SER A 199
SHEET 3 AA9 4 ARG A 432 ILE A 434 -1 O ILE A 434 N VAL A 120
SHEET 4 AA9 4 ILE A 423 ASN A 425 -1 N ILE A 424 O ALA A 433
SHEET 1 AB1 3 VAL A 242 VAL A 245 0
SHEET 2 AB1 3 ALA A 224 CYS A 228 -1 N ILE A 225 O VAL A 245
SHEET 3 AB1 3 TYR A 486 VAL A 489 -1 O VAL A 489 N ALA A 224
SHEET 1 AB2 7 LEU A 259 LEU A 261 0
SHEET 2 AB2 7 ILE A 443 ARG A 456 -1 O THR A 450 N LEU A 260
SHEET 3 AB2 7 ILE A 284 ARG A 298 -1 N CYS A 296 O CYS A 445
SHEET 4 AB2 7 GLN A 328 ASN A 334 -1 O HIS A 330 N THR A 297
SHEET 5 AB2 7 THR A 413 ILE A 420 -1 O ILE A 414 N ILE A 333
SHEET 6 AB2 7 GLU A 381 CYS A 385 -1 N TYR A 384 O LYS A 419
SHEET 7 AB2 7 HIS A 374 CYS A 378 -1 N CYS A 378 O GLU A 381
SHEET 1 AB3 7 ILE A 271 SER A 274 0
SHEET 2 AB3 7 ILE A 284 ARG A 298 -1 O ILE A 285 N ARG A 273
SHEET 3 AB3 7 ILE A 443 ARG A 456 -1 O CYS A 445 N CYS A 296
SHEET 4 AB3 7 THR A 465 PRO A 470 -1 O ARG A 469 N LEU A 455
SHEET 5 AB3 7 THR A 358 PHE A 361 1 N LYS A 360 O PHE A 468
SHEET 6 AB3 7 GLY A 393 ARG A 396 -1 O TYR A 395 N ILE A 359
SHEET 7 AB3 7 THR A 399 HIS A 405 -1 O THR A 399 N ARG A 396
SSBOND 1 CYS D 54 CYS D 74 1555 1555 2.03
SSBOND 2 CYS D 119 CYS D 205 1555 1555 2.03
SSBOND 3 CYS D 218 CYS D 247 1555 1555 2.03
SSBOND 4 CYS D 228 CYS D 239 1555 1555 2.03
SSBOND 5 CYS D 296 CYS D 331 1555 1555 2.03
SSBOND 6 CYS D 378 CYS D 445 1555 1555 2.03
SSBOND 7 CYS D 385 CYS D 418 1555 1555 2.03
SSBOND 8 CYS A 54 CYS A 74 1555 1555 2.03
SSBOND 9 CYS A 119 CYS A 205 1555 1555 2.03
SSBOND 10 CYS A 218 CYS A 247 1555 1555 2.03
SSBOND 11 CYS A 228 CYS A 239 1555 1555 2.04
SSBOND 12 CYS A 296 CYS A 331 1555 1555 2.03
SSBOND 13 CYS A 378 CYS A 445 1555 1555 2.03
SSBOND 14 CYS A 385 CYS A 418 1555 1555 2.03
CRYST1 67.378 127.517 192.945 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 0.014842 0.000000 0.000000 0.00000
SCALE2 0.000000 0.007842 0.000000 0.00000
SCALE3 0.000000 0.000000 0.005183 0.00000