HEADER IMMUNE SYSTEM/TRANSCRIPTION INHIBITOR 23-FEB-12 4DVR TITLE CRYSTAL STRUCTURE OF YU2 GP120 CORE IN COMPLEX WITH FAB 48D AND NBD- TITLE 2 557 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENVELOPE GLYCOPROTEIN GP120; COMPND 3 CHAIN: G; COMPND 4 FRAGMENT: UNP RESIDUES 82-122; 199-297; 319-479; COMPND 5 SYNONYM: ENV POLYPROTEIN,ENV POLYPROTEIN,ENV POLYPROTEIN; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: FAB 48D LIGHT CHAIN; COMPND 9 CHAIN: L; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: FAB 48D HEAVY CHAIN; COMPND 13 CHAIN: H; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 GROUP M SOURCE 3 SUBTYPE B (ISOLATE YU-2); SOURCE 4 ORGANISM_COMMON: HIV-1; SOURCE 5 ORGANISM_TAXID: 362651; SOURCE 6 STRAIN: ISOLATE YU-2; SOURCE 7 GENE: ENV; SOURCE 8 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 9 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 11 EXPRESSION_SYSTEM_CELL_LINE: HEK293F; SOURCE 12 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 13 EXPRESSION_SYSTEM_PLASMID: PVRC8400; SOURCE 14 MOL_ID: 2; SOURCE 15 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 16 ORGANISM_COMMON: HUMAN; SOURCE 17 ORGANISM_TAXID: 9606; SOURCE 18 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 19 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 20 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 21 MOL_ID: 3; SOURCE 22 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 23 ORGANISM_COMMON: HUMAN; SOURCE 24 ORGANISM_TAXID: 9606; SOURCE 25 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 26 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 27 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS HIV-1 GP120, CD4 BINDING SITE, NBD-557, IMMUNE SYSTEM-TRANSCRIPTION KEYWDS 2 INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.D.KWON,P.D.KWONG REVDAT 7 13-SEP-23 4DVR 1 REMARK REVDAT 6 19-MAY-21 4DVR 1 SOURCE HETSYN REVDAT 5 29-JUL-20 4DVR 1 COMPND REMARK HETNAM LINK REVDAT 5 2 1 SITE REVDAT 4 31-MAY-17 4DVR 1 COMPND SOURCE DBREF REVDAT 3 17-DEC-14 4DVR 1 HETSYN COMPND REVDAT 2 19-MAR-14 4DVR 1 JRNL REVDAT 1 27-FEB-13 4DVR 0 JRNL AUTH Y.D.KWON,J.M.LALONDE,Y.YANG,M.A.ELBAN,A.SUGAWARA, JRNL AUTH 2 J.R.COURTER,D.M.JONES,A.B.SMITH,A.K.DEBNATH,P.D.KWONG JRNL TITL CRYSTAL STRUCTURES OF HIV-1 GP120 ENVELOPE GLYCOPROTEIN IN JRNL TITL 2 COMPLEX WITH NBD ANALOGUES THAT TARGET THE CD4-BINDING SITE. JRNL REF PLOS ONE V. 9 85940 2014 JRNL REFN ESSN 1932-6203 JRNL PMID 24489681 JRNL DOI 10.1371/JOURNAL.PONE.0085940 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8_1069 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.40 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.420 REMARK 3 COMPLETENESS FOR RANGE (%) : 87.8 REMARK 3 NUMBER OF REFLECTIONS : 24129 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.233 REMARK 3 R VALUE (WORKING SET) : 0.228 REMARK 3 FREE R VALUE : 0.289 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.160 REMARK 3 FREE R VALUE TEST SET COUNT : 1970 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 49.4776 - 6.0139 0.98 1910 169 0.2117 0.2651 REMARK 3 2 6.0139 - 4.7747 0.99 1833 164 0.1957 0.2446 REMARK 3 3 4.7747 - 4.1715 0.99 1803 159 0.1835 0.2302 REMARK 3 4 4.1715 - 3.7902 0.99 1793 160 0.2098 0.2926 REMARK 3 5 3.7902 - 3.5186 0.99 1793 159 0.2337 0.2584 REMARK 3 6 3.5186 - 3.3112 0.99 1758 156 0.2444 0.3366 REMARK 3 7 3.3112 - 3.1454 0.97 1721 153 0.2634 0.3036 REMARK 3 8 3.1454 - 3.0085 0.94 1691 151 0.2928 0.3515 REMARK 3 9 3.0085 - 2.8927 0.88 1576 141 0.2947 0.4087 REMARK 3 10 2.8927 - 2.7929 0.84 1482 133 0.3060 0.4086 REMARK 3 11 2.7929 - 2.7056 0.76 1363 122 0.3084 0.4188 REMARK 3 12 2.7056 - 2.6283 0.72 1264 113 0.3217 0.3581 REMARK 3 13 2.6283 - 2.5591 0.66 1163 100 0.3145 0.4125 REMARK 3 14 2.5591 - 2.4966 0.56 1009 90 0.3274 0.4201 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) : 0.460 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 35.420 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 56.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 71.82 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.87450 REMARK 3 B22 (A**2) : -0.30030 REMARK 3 B33 (A**2) : -2.57420 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 : 0.001 5792 REMARK 3 ANGLE : 0.359 7862 REMARK 3 CHIRALITY : 0.022 895 REMARK 3 PLANARITY : 0.002 998 REMARK 3 DIHEDRAL : 7.027 2116 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN G AND (RESID 1:252 OR RESID 474:492) REMARK 3 ORIGIN FOR THE GROUP (A): 43.4667 6.0101 87.9153 REMARK 3 T TENSOR REMARK 3 T11: 0.4390 T22: 0.4890 REMARK 3 T33: 0.3686 T12: -0.0278 REMARK 3 T13: 0.0039 T23: -0.1111 REMARK 3 L TENSOR REMARK 3 L11: 4.3939 L22: 6.6073 REMARK 3 L33: 3.6797 L12: -3.2548 REMARK 3 L13: 2.3038 L23: -1.5238 REMARK 3 S TENSOR REMARK 3 S11: 0.1752 S12: -0.0979 S13: -0.0567 REMARK 3 S21: -0.0924 S22: -0.0224 S23: -0.4238 REMARK 3 S31: 0.1660 S32: 0.3224 S33: -0.1392 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN G AND RESID 253:473 REMARK 3 ORIGIN FOR THE GROUP (A): 41.9438 21.6070 100.7025 REMARK 3 T TENSOR REMARK 3 T11: 0.4549 T22: 0.3299 REMARK 3 T33: 0.3893 T12: -0.0504 REMARK 3 T13: 0.0162 T23: -0.0321 REMARK 3 L TENSOR REMARK 3 L11: 3.9122 L22: 3.8768 REMARK 3 L33: 3.6564 L12: -1.3859 REMARK 3 L13: 0.4538 L23: -0.2043 REMARK 3 S TENSOR REMARK 3 S11: -0.0349 S12: -0.2795 S13: 0.1358 REMARK 3 S21: 0.3244 S22: 0.2250 S23: -0.4710 REMARK 3 S31: -0.1653 S32: 0.1099 S33: -0.1996 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN H AND RESID 1:118 REMARK 3 ORIGIN FOR THE GROUP (A): 23.2974 45.8486 80.9719 REMARK 3 T TENSOR REMARK 3 T11: 0.4737 T22: 0.4931 REMARK 3 T33: 0.3524 T12: 0.0477 REMARK 3 T13: 0.0158 T23: 0.0291 REMARK 3 L TENSOR REMARK 3 L11: 4.4743 L22: 7.7229 REMARK 3 L33: 4.9214 L12: -0.4195 REMARK 3 L13: 2.2937 L23: -2.8066 REMARK 3 S TENSOR REMARK 3 S11: -0.3318 S12: -0.0699 S13: -0.0045 REMARK 3 S21: 0.7412 S22: 0.4413 S23: 0.0364 REMARK 3 S31: -0.1766 S32: -0.0215 S33: -0.1119 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN H AND RESID 119:219 REMARK 3 ORIGIN FOR THE GROUP (A): 2.5121 69.0879 65.1466 REMARK 3 T TENSOR REMARK 3 T11: 0.6729 T22: 0.6693 REMARK 3 T33: 0.3742 T12: 0.1294 REMARK 3 T13: 0.0154 T23: 0.0102 REMARK 3 L TENSOR REMARK 3 L11: 7.1487 L22: 4.3729 REMARK 3 L33: 3.6958 L12: -0.1064 REMARK 3 L13: 2.1727 L23: -0.6992 REMARK 3 S TENSOR REMARK 3 S11: -0.1638 S12: -0.5053 S13: 0.2242 REMARK 3 S21: 0.1004 S22: 0.0405 S23: 0.2325 REMARK 3 S31: -0.7514 S32: -0.8182 S33: 0.1847 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN L AND RESID 1:108 REMARK 3 ORIGIN FOR THE GROUP (A): 3.9875 34.7810 76.4624 REMARK 3 T TENSOR REMARK 3 T11: 0.4198 T22: 0.6747 REMARK 3 T33: 0.9283 T12: -0.1262 REMARK 3 T13: -0.0510 T23: 0.3924 REMARK 3 L TENSOR REMARK 3 L11: 1.7299 L22: 0.3289 REMARK 3 L33: 2.1675 L12: -0.7662 REMARK 3 L13: 1.9664 L23: -0.8376 REMARK 3 S TENSOR REMARK 3 S11: 0.0586 S12: -0.4352 S13: -1.0138 REMARK 3 S21: 0.1836 S22: 0.6610 S23: 1.0092 REMARK 3 S31: 0.1456 S32: -0.6500 S33: -0.4383 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN L AND RESID 109:212 REMARK 3 ORIGIN FOR THE GROUP (A): -0.1816 60.9847 51.7526 REMARK 3 T TENSOR REMARK 3 T11: 0.5335 T22: 0.4290 REMARK 3 T33: 0.4090 T12: 0.1257 REMARK 3 T13: 0.0824 T23: 0.0411 REMARK 3 L TENSOR REMARK 3 L11: 5.3603 L22: 8.1240 REMARK 3 L33: 5.2099 L12: 2.8943 REMARK 3 L13: -0.3762 L23: -3.1084 REMARK 3 S TENSOR REMARK 3 S11: 0.1881 S12: -0.1572 S13: -0.0655 REMARK 3 S21: -0.2347 S22: -0.0151 S23: 0.5624 REMARK 3 S31: -0.7008 S32: -0.2828 S33: -0.1946 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 4DVR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-MAR-12. REMARK 100 THE DEPOSITION ID IS D_1000070843. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-JUN-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 300 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24559 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 49.400 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 89.7 REMARK 200 DATA REDUNDANCY : 4.600 REMARK 200 R MERGE (I) : 0.13400 REMARK 200 R SYM (I) : 0.15500 REMARK 200 FOR THE DATA SET : 11.0400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 62.9 REMARK 200 DATA REDUNDANCY IN SHELL : 1.80 REMARK 200 R MERGE FOR SHELL (I) : 0.49700 REMARK 200 R SYM FOR SHELL (I) : 0.46000 REMARK 200 FOR SHELL : 2.200 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: PDB ENTRY 1RZK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG3350, 5% ISO-PROPANOL, 0.1M REMARK 280 TRIS, PH 8.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 26.72250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 65.34100 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 54.86900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 65.34100 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.72250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 54.86900 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 300 REMARK: MONOMER 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: 7880 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 33050 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: G, L, H 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 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 GLU G 83 REMARK 465 VAL G 84 REMARK 465 LYS G 85 REMARK 465 LEU G 86 REMARK 465 GLU G 87 REMARK 465 ASN G 88 REMARK 465 VAL G 89 REMARK 465 GLY G 318 REMARK 465 GLY G 319 REMARK 465 SER G 320 REMARK 465 GLY G 321 REMARK 465 SER G 322 REMARK 465 GLY G 323 REMARK 465 ARG G 405 REMARK 465 LYS G 406 REMARK 465 LEU G 407 REMARK 465 ASN G 408 REMARK 465 ASN G 409 REMARK 465 THR G 410 REMARK 465 GLY G 411 REMARK 465 GLY G 458 REMARK 465 GLY G 459 REMARK 465 LYS G 460 REMARK 465 ASP G 461 REMARK 465 THR G 462 REMARK 465 ASP L 1 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ASP G 230 OD2 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 HOH G 647 O HOH G 650 1.86 REMARK 500 O HOH G 643 O HOH G 644 1.90 REMARK 500 SG CYS G 119 CB CYS G 205 1.94 REMARK 500 OG SER H 7 O HOH H 302 2.00 REMARK 500 ND2 ASN G 289 C2 NAG G 504 2.04 REMARK 500 OH TYR L 185 O HOH L 320 2.06 REMARK 500 N LYS G 97 O HOH G 617 2.06 REMARK 500 O HOH H 323 O HOH H 329 2.09 REMARK 500 N ASP H 214 O HOH H 308 2.11 REMARK 500 NH1 ARG G 419 O HOH G 618 2.15 REMARK 500 O TYR G 435 O HOH G 637 2.15 REMARK 500 O PHE G 233 NH1 ARG G 273 2.15 REMARK 500 NE2 GLN L 123 O HOH L 315 2.16 REMARK 500 O HOH H 326 O HOH H 328 2.16 REMARK 500 OG SER L 181 OD1 ASP L 184 2.16 REMARK 500 O GLY G 472 O HOH G 639 2.16 REMARK 500 N LYS G 232 O HOH G 623 2.18 REMARK 500 OE1 GLU G 211 O HOH G 632 2.19 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 LEU G 116 75.14 -107.20 REMARK 500 ASN G 229 64.04 -112.99 REMARK 500 ASN G 241 79.41 -109.00 REMARK 500 PRO G 253 81.86 -59.52 REMARK 500 GLN G 258 -60.61 63.88 REMARK 500 GLU G 268 -79.77 -98.21 REMARK 500 ASN G 276 88.73 -169.35 REMARK 500 SER G 387 59.89 -114.91 REMARK 500 SER L 30 -121.61 56.97 REMARK 500 SER L 52 -45.18 -163.65 REMARK 500 PRO L 59 150.48 -47.38 REMARK 500 ALA L 84 -163.04 -170.53 REMARK 500 ALA L 91 34.18 -154.27 REMARK 500 SER L 93 -58.74 -143.80 REMARK 500 ASN L 137 90.19 52.46 REMARK 500 PRO L 140 -165.21 -70.00 REMARK 500 LYS L 189 -44.59 -132.14 REMARK 500 PRO H 14 97.26 -58.07 REMARK 500 THR H 28 98.27 -65.72 REMARK 500 LEU H 130 74.43 -113.45 REMARK 500 SER H 133 -177.45 -171.87 REMARK 500 SER H 136 21.20 -143.57 REMARK 500 ASP H 150 71.87 58.17 REMARK 500 PRO H 153 -158.64 -95.97 REMARK 500 THR H 197 -46.38 -134.93 REMARK 500 REMARK 500 REMARK: NULL REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE CRYSTALLIZED SEQUENCE WAS CONSTRUCTED BY DELETION OF N-TERMINAL REMARK 999 1-43, BY REPLACING THE V1/V2 REGIONS WITH A GG LINKER, AND REMARK 999 REPLACING V3 REGION WITH A LINKER GGSGSG DBREF 4DVR G 83 123 UNP P35961 ENV_HV1Y2 82 122 DBREF 4DVR G 199 301 UNP P35961 ENV_HV1Y2 195 297 DBREF 4DVR G 324 492 UNP P35961 ENV_HV1Y2 319 479 DBREF 4DVR L 1 212 PDB 4DVR 4DVR 1 212 DBREF 4DVR H 1 219 PDB 4DVR 4DVR 1 219 SEQADV 4DVR GLY G 124 UNP P35961 LINKER SEQADV 4DVR GLY G 198 UNP P35961 LINKER SEQADV 4DVR GLY G 318 UNP P35961 LINKER SEQADV 4DVR GLY G 319 UNP P35961 LINKER SEQADV 4DVR SER G 320 UNP P35961 LINKER SEQADV 4DVR GLY G 321 UNP P35961 LINKER SEQADV 4DVR SER G 322 UNP P35961 LINKER SEQADV 4DVR GLY G 323 UNP P35961 LINKER SEQRES 1 G 313 GLU VAL LYS LEU GLU ASN VAL THR GLU ASN PHE ASN MET SEQRES 2 G 313 TRP LYS ASN ASN MET VAL GLU GLN MET HIS GLU ASP ILE SEQRES 3 G 313 ILE SER LEU TRP ASP GLN SER LEU LYS PRO CYS VAL LYS SEQRES 4 G 313 LEU THR GLY GLY SER VAL ILE THR GLN ALA CYS PRO LYS SEQRES 5 G 313 VAL SER PHE GLU PRO ILE PRO ILE HIS TYR CYS ALA PRO SEQRES 6 G 313 ALA GLY PHE ALA ILE LEU LYS CYS ASN ASP LYS LYS PHE SEQRES 7 G 313 ASN GLY THR GLY PRO CYS THR ASN VAL SER THR VAL GLN SEQRES 8 G 313 CYS THR HIS GLY ILE ARG PRO VAL VAL SER THR GLN LEU SEQRES 9 G 313 LEU LEU ASN GLY SER LEU ALA GLU GLU GLU ILE VAL ILE SEQRES 10 G 313 ARG SER GLU ASN PHE THR ASN ASN ALA LYS THR ILE ILE SEQRES 11 G 313 VAL GLN LEU ASN GLU SER VAL VAL ILE ASN CYS THR ARG SEQRES 12 G 313 PRO ASN ASN GLY GLY SER GLY SER GLY GLY ASP ILE ARG SEQRES 13 G 313 GLN ALA HIS CYS ASN LEU SER LYS THR GLN TRP GLU ASN SEQRES 14 G 313 THR LEU GLU GLN ILE ALA ILE LYS LEU LYS GLU GLN PHE SEQRES 15 G 313 GLY ASN ASN LYS THR ILE ILE PHE ASN PRO SER SER GLY SEQRES 16 G 313 GLY ASP PRO GLU ILE VAL THR HIS SER PHE ASN CYS GLY SEQRES 17 G 313 GLY GLU PHE PHE TYR CYS ASN SER THR GLN LEU PHE THR SEQRES 18 G 313 TRP ASN ASP THR ARG LYS LEU ASN ASN THR GLY ARG ASN SEQRES 19 G 313 ILE THR LEU PRO CYS ARG ILE LYS GLN ILE ILE ASN MET SEQRES 20 G 313 TRP GLN GLU VAL GLY LYS ALA MET TYR ALA PRO PRO ILE SEQRES 21 G 313 ARG GLY GLN ILE ARG CYS SER SER ASN ILE THR GLY LEU SEQRES 22 G 313 LEU LEU THR ARG ASP GLY GLY LYS ASP THR ASN GLY THR SEQRES 23 G 313 GLU ILE PHE ARG PRO GLY GLY GLY ASP MET ARG ASP ASN SEQRES 24 G 313 TRP ARG SER GLU LEU TYR LYS TYR LYS VAL VAL LYS ILE SEQRES 25 G 313 GLU SEQRES 1 L 212 ASP ILE GLN MET THR GLN SER PRO SER SER VAL SER ALA SEQRES 2 L 212 SER VAL GLY ASP ARG VAL THR ILE THR CYS ARG ALA SER SEQRES 3 L 212 GLN ASP ILE SER THR TRP LEU ALA TRP TYR GLN GLN LYS SEQRES 4 L 212 PRO GLY LYS ALA PRO LYS LEU LEU ILE TYR ALA ALA SER SEQRES 5 L 212 THR LEU GLN SER GLY VAL PRO SER ARG PHE SER GLY SER SEQRES 6 L 212 GLY SER GLY THR ASP PHE SER LEU THR ILE ASN SER LEU SEQRES 7 L 212 GLN PRO GLU ASP PHE ALA THR TYR TYR CYS GLN GLN ALA SEQRES 8 L 212 ASN SER PHE PHE THR PHE GLY GLY GLY THR LYS VAL GLU SEQRES 9 L 212 ILE LYS ARG THR VAL ALA ALA PRO SER VAL PHE ILE PHE SEQRES 10 L 212 PRO PRO SER ASP GLU GLN LEU LYS SER GLY THR ALA SER SEQRES 11 L 212 VAL VAL CYS LEU LEU ASN ASN PHE TYR PRO ARG GLU ALA SEQRES 12 L 212 LYS VAL GLN TRP LYS VAL ASP ASN ALA LEU GLN SER GLY SEQRES 13 L 212 ASN SER GLN GLU SER VAL THR GLU GLN ASP SER LYS ASP SEQRES 14 L 212 SER THR TYR SER LEU SER SER THR LEU THR LEU SER LYS SEQRES 15 L 212 ALA ASP TYR GLU LYS HIS LYS LEU TYR ALA CYS GLU VAL SEQRES 16 L 212 THR HIS GLN GLY LEU SER SER PRO VAL THR LYS SER PHE SEQRES 17 L 212 ASN ARG GLY GLU SEQRES 1 H 219 GLU VAL GLN LEU VAL GLN SER GLY ALA GLU VAL LYS LYS SEQRES 2 H 219 PRO GLY ALA THR VAL LYS ILE SER CYS LYS ALA SER GLY SEQRES 3 H 219 TYR THR PHE SER ASP PHE TYR MET TYR TRP VAL ARG GLN SEQRES 4 H 219 ALA PRO GLY LYS GLY LEU GLU TRP MET GLY LEU ILE ASP SEQRES 5 H 219 PRO GLU ASP ALA ASP THR MET TYR ALA GLU LYS PHE ARG SEQRES 6 H 219 GLY ARG VAL THR ILE THR ALA ASP THR SER THR ASP THR SEQRES 7 H 219 GLY TYR LEU GLU LEU SER SER LEU ARG SER GLU ASP THR SEQRES 8 H 219 ALA VAL TYR TYR CYS ALA ALA ASP PRO TRP GLU LEU ASN SEQRES 9 H 219 ALA PHE ASN VAL TRP GLY GLN GLY THR LEU VAL SER VAL SEQRES 10 H 219 SER SER ALA SER THR LYS GLY PRO SER VAL PHE PRO LEU SEQRES 11 H 219 ALA PRO SER SER LYS SER THR SER GLY GLY THR ALA ALA SEQRES 12 H 219 LEU GLY CYS LEU VAL LYS ASP TYR PHE PRO GLU PRO VAL SEQRES 13 H 219 THR VAL SER TRP ASN SER GLY ALA LEU THR SER GLY VAL SEQRES 14 H 219 HIS THR PHE PRO ALA VAL LEU GLN SER SER GLY LEU TYR SEQRES 15 H 219 SER LEU SER SER VAL VAL THR VAL PRO SER SER SER LEU SEQRES 16 H 219 GLY THR GLN THR TYR ILE CYS ASN VAL ASN HIS LYS PRO SEQRES 17 H 219 SER ASN THR LYS VAL ASP LYS LYS VAL GLU PRO MODRES 4DVR ASN G 289 ASN GLYCOSYLATION SITE MODRES 4DVR ASN G 276 ASN GLYCOSYLATION SITE MODRES 4DVR ASN G 295 ASN GLYCOSYLATION SITE MODRES 4DVR ASN G 386 ASN GLYCOSYLATION SITE MODRES 4DVR ASN G 234 ASN GLYCOSYLATION SITE MODRES 4DVR ASN G 262 ASN GLYCOSYLATION SITE MODRES 4DVR ASN G 448 ASN GLYCOSYLATION SITE HET NAG G 501 14 HET NAG G 502 14 HET NAG G 503 14 HET NAG G 504 14 HET NAG G 505 14 HET NAG G 506 14 HET NAG G 507 14 HET 0LY G 508 47 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM 0LY N-(4-BROMOPHENYL)-N'-(2,2,6,6-TETRAMETHYLPIPERIDIN-4- HETNAM 2 0LY YL)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 HETSYN 0LY NBD-557 FORMUL 4 NAG 7(C8 H15 N O6) FORMUL 11 0LY C17 H24 BR N3 O2 FORMUL 12 HOH *113(H2 O) HELIX 1 1 ASN G 99 LEU G 116 1 18 HELIX 2 2 LYS G 335 GLY G 354 1 20 HELIX 3 3 ASP G 368 THR G 373 1 6 HELIX 4 4 ASP G 474 SER G 481 1 8 HELIX 5 5 SER L 120 GLY L 127 1 8 HELIX 6 6 LYS L 182 LYS L 187 1 6 HELIX 7 7 THR H 28 PHE H 32 5 5 HELIX 8 8 ARG H 87 THR H 91 5 5 HELIX 9 9 SER H 193 LEU H 195 5 3 HELIX 10 10 LYS H 207 ASN H 210 5 4 SHEET 1 A 2 ASN G 92 ASN G 94 0 SHEET 2 A 2 THR G 236 PRO G 238 -1 O GLY G 237 N PHE G 93 SHEET 1 B 4 VAL G 200 THR G 202 0 SHEET 2 B 4 VAL G 120 LEU G 122 -1 N LYS G 121 O ILE G 201 SHEET 3 B 4 LYS G 432 MET G 434 -1 O LYS G 432 N LEU G 122 SHEET 4 B 4 ILE G 423 ASN G 425 -1 N ILE G 424 O ALA G 433 SHEET 1 C 3 VAL G 242 VAL G 245 0 SHEET 2 C 3 PHE G 223 CYS G 228 -1 N LYS G 227 O SER G 243 SHEET 3 C 3 TYR G 486 LYS G 490 -1 O VAL G 489 N ALA G 224 SHEET 1 D 5 LEU G 259 LEU G 261 0 SHEET 2 D 5 ILE G 443 ARG G 456 -1 O GLY G 451 N LEU G 260 SHEET 3 D 5 ILE G 284 ARG G 298 -1 N ILE G 284 O LEU G 454 SHEET 4 D 5 GLU G 466 PRO G 470 0 SHEET 5 D 5 ILE G 359 PHE G 361 1 N ILE G 360 O GLU G 466 SHEET 1 E 7 VAL G 271 SER G 274 0 SHEET 2 E 7 ILE G 284 ARG G 298 -1 O ILE G 285 N ARG G 273 SHEET 3 E 7 ILE G 443 ARG G 456 -1 O LEU G 454 N ILE G 284 SHEET 4 E 7 GLN G 328 SER G 334 0 SHEET 5 E 7 ASN G 413 LYS G 421 -1 O LEU G 416 N CYS G 331 SHEET 6 E 7 GLU G 381 CYS G 385 -1 N TYR G 384 O ARG G 419 SHEET 7 E 7 HIS G 374 CYS G 378 -1 N PHE G 376 O PHE G 383 SHEET 1 F 4 MET L 4 SER L 7 0 SHEET 2 F 4 VAL L 19 ALA L 25 -1 O ARG L 24 N THR L 5 SHEET 3 F 4 ASP L 70 ILE L 75 -1 O LEU L 73 N ILE L 21 SHEET 4 F 4 PHE L 62 SER L 67 -1 N SER L 63 O THR L 74 SHEET 1 G 6 SER L 10 ALA L 13 0 SHEET 2 G 6 THR L 101 ILE L 105 1 O GLU L 104 N VAL L 11 SHEET 3 G 6 THR L 85 GLN L 90 -1 N TYR L 86 O THR L 101 SHEET 4 G 6 LEU L 33 GLN L 38 -1 N GLN L 38 O THR L 85 SHEET 5 G 6 LYS L 45 TYR L 49 -1 O ILE L 48 N TRP L 35 SHEET 6 G 6 THR L 53 LEU L 54 -1 O THR L 53 N TYR L 49 SHEET 1 H 4 SER L 113 PHE L 117 0 SHEET 2 H 4 THR L 128 PHE L 138 -1 O LEU L 134 N PHE L 115 SHEET 3 H 4 TYR L 172 SER L 181 -1 O LEU L 178 N VAL L 131 SHEET 4 H 4 SER L 158 VAL L 162 -1 N GLN L 159 O THR L 177 SHEET 1 I 4 ALA L 152 GLN L 154 0 SHEET 2 I 4 LYS L 144 VAL L 149 -1 N VAL L 149 O ALA L 152 SHEET 3 I 4 LEU L 190 THR L 196 -1 O ALA L 192 N LYS L 148 SHEET 4 I 4 VAL L 204 ASN L 209 -1 O VAL L 204 N VAL L 195 SHEET 1 J 4 GLN H 3 GLN H 6 0 SHEET 2 J 4 VAL H 18 SER H 25 -1 O LYS H 23 N VAL H 5 SHEET 3 J 4 THR H 78 LEU H 83 -1 O LEU H 81 N ILE H 20 SHEET 4 J 4 VAL H 68 ASP H 73 -1 N THR H 71 O TYR H 80 SHEET 1 K 6 GLU H 10 LYS H 12 0 SHEET 2 K 6 THR H 113 VAL H 117 1 O SER H 116 N LYS H 12 SHEET 3 K 6 ALA H 92 ALA H 98 -1 N ALA H 92 O VAL H 115 SHEET 4 K 6 MET H 34 GLN H 39 -1 N VAL H 37 O TYR H 95 SHEET 5 K 6 LEU H 45 ASP H 52 -1 O MET H 48 N TRP H 36 SHEET 6 K 6 ASP H 57 TYR H 60 -1 O ASP H 57 N ASP H 52 SHEET 1 L 4 GLU H 10 LYS H 12 0 SHEET 2 L 4 THR H 113 VAL H 117 1 O SER H 116 N LYS H 12 SHEET 3 L 4 ALA H 92 ALA H 98 -1 N ALA H 92 O VAL H 115 SHEET 4 L 4 VAL H 108 TRP H 109 -1 O VAL H 108 N ALA H 98 SHEET 1 M 4 SER H 126 LEU H 130 0 SHEET 2 M 4 THR H 141 TYR H 151 -1 O LEU H 147 N PHE H 128 SHEET 3 M 4 TYR H 182 PRO H 191 -1 O VAL H 188 N LEU H 144 SHEET 4 M 4 VAL H 169 THR H 171 -1 N HIS H 170 O VAL H 187 SHEET 1 N 4 THR H 137 SER H 138 0 SHEET 2 N 4 THR H 141 TYR H 151 -1 O THR H 141 N SER H 138 SHEET 3 N 4 TYR H 182 PRO H 191 -1 O VAL H 188 N LEU H 144 SHEET 4 N 4 VAL H 175 LEU H 176 -1 N VAL H 175 O SER H 183 SHEET 1 O 3 THR H 157 TRP H 160 0 SHEET 2 O 3 TYR H 200 HIS H 206 -1 O ASN H 203 N SER H 159 SHEET 3 O 3 THR H 211 VAL H 217 -1 O THR H 211 N HIS H 206 SSBOND 1 CYS G 119 CYS G 205 1555 1555 2.03 SSBOND 2 CYS G 218 CYS G 247 1555 1555 2.03 SSBOND 3 CYS G 228 CYS G 239 1555 1555 2.03 SSBOND 4 CYS G 296 CYS G 331 1555 1555 2.03 SSBOND 5 CYS G 378 CYS G 445 1555 1555 2.03 SSBOND 6 CYS G 385 CYS G 418 1555 1555 2.03 SSBOND 7 CYS L 23 CYS L 88 1555 1555 2.03 SSBOND 8 CYS L 133 CYS L 193 1555 1555 2.03 SSBOND 9 CYS H 22 CYS H 96 1555 1555 2.03 SSBOND 10 CYS H 146 CYS H 202 1555 1555 2.03 LINK ND2 ASN G 234 C1 NAG G 501 1555 1555 1.44 LINK ND2 ASN G 262 C1 NAG G 502 1555 1555 1.44 LINK ND2 ASN G 276 C1 NAG G 503 1555 1555 1.44 LINK ND2 ASN G 289 C1 NAG G 504 1555 1555 1.44 LINK ND2 ASN G 295 C1 NAG G 505 1555 1555 1.44 LINK ND2 ASN G 386 C1 NAG G 506 1555 1555 1.44 LINK ND2 ASN G 448 C1 NAG G 507 1555 1555 1.44 CISPEP 1 SER L 7 PRO L 8 0 -1.33 CISPEP 2 TYR L 139 PRO L 140 0 0.90 CISPEP 3 PHE H 152 PRO H 153 0 -2.40 CISPEP 4 GLU H 154 PRO H 155 0 -0.86 CRYST1 53.445 109.738 130.682 90.00 90.00 90.00 P 21 21 21 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 0.018711 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009113 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007652 0.00000