HEADER VIRAL PROTEIN/INHIBITOR 10-JAN-19 6J5E TITLE CRYSTAL STRUCTURE OF HIV-1 FUSION INHIBITOR SC29EK COMPLEXED WITH GP41 TITLE 2 NHR (N44) COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENVELOPE GLYCOPROTEIN; COMPND 3 CHAIN: G, I, K; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: SC29EK; COMPND 7 CHAIN: H, J, L; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; SOURCE 3 ORGANISM_TAXID: 11676; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 MOL_ID: 2; SOURCE 7 SYNTHETIC: YES; SOURCE 8 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; SOURCE 9 ORGANISM_TAXID: 11676 KEYWDS HIV FUSION INHIBITOR, SIX HELIX BUNDLE., VIRAL PROTEIN-INHIBITOR KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Z.X.LIU,X.Z.GENG,B.QIN,S.CUI REVDAT 3 23-OCT-24 6J5E 1 REMARK REVDAT 2 22-NOV-23 6J5E 1 REMARK REVDAT 1 15-JAN-20 6J5E 0 JRNL AUTH Z.X.LIU,X.Z.GENG,B.QIN,S.CUI JRNL TITL CRYSTAL STRUCTURE OF HIV-1 FUSION INHIBITOR SC29EK COMPLEXED JRNL TITL 2 WITH GP41 NHR (N44) JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.33 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???) 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) : 2.33 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.83 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 20260 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.236 REMARK 3 R VALUE (WORKING SET) : 0.233 REMARK 3 FREE R VALUE : 0.286 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.380 REMARK 3 FREE R VALUE TEST SET COUNT : 1090 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 38.8306 - 4.6573 0.98 2400 132 0.2296 0.2591 REMARK 3 2 4.6573 - 3.6975 0.99 2422 144 0.1912 0.2625 REMARK 3 3 3.6975 - 3.2304 0.99 2442 138 0.2272 0.2834 REMARK 3 4 3.2304 - 2.9352 1.00 2440 144 0.2624 0.3411 REMARK 3 5 2.9352 - 2.7248 1.00 2418 130 0.2453 0.3065 REMARK 3 6 2.7248 - 2.5642 1.00 2439 142 0.2837 0.3301 REMARK 3 7 2.5642 - 2.4358 1.00 2395 162 0.2913 0.3181 REMARK 3 8 2.4358 - 2.3298 0.89 2214 98 0.3234 0.3876 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) : 0.310 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.170 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 57.99 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 : 0.003 1781 REMARK 3 ANGLE : 0.491 2382 REMARK 3 CHIRALITY : 0.030 262 REMARK 3 PLANARITY : 0.002 299 REMARK 3 DIHEDRAL : 15.461 1110 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 6J5E COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-JAN-19. REMARK 100 THE DEPOSITION ID IS D_1300010389. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-JUL-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL 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) : 0.979150 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 : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20721 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.330 REMARK 200 RESOLUTION RANGE LOW (A) : 38.825 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 3.190 REMARK 200 R MERGE (I) : 0.08300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.1600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.33 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.44 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.86100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.530 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: 5H0N REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.76 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M PH3.5 CITRIC ACID, 16%(W/V) REMARK 280 PEG8000, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K 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 18.25000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 85.75150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.93000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 85.75150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.25000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 19.93000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 11620 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10930 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -102.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: G, H, I, J, K, 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 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 THR G 27 REMARK 465 VAL G 28 REMARK 465 GLN G 29 REMARK 465 LEU G 70 REMARK 465 THR I 27 REMARK 465 VAL I 28 REMARK 465 GLN I 29 REMARK 465 ALA I 30 REMARK 465 ARG I 31 REMARK 465 GLN I 32 REMARK 465 LEU I 70 REMARK 465 ACE J 116 REMARK 465 THR K 27 REMARK 465 VAL K 28 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 HD22 ASN H 145 O HOH H 201 1.41 REMARK 500 OD1 ASN K 43 O HOH K 101 2.13 REMARK 500 OE1 GLN K 41 O HOH K 102 2.15 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 LYS J 144 -69.92 -166.73 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH H 203 DISTANCE = 5.86 ANGSTROMS DBREF 6J5E G 27 70 UNP Q1HMR5 Q1HMR5_9HIV1 27 70 DBREF 6J5E H 116 145 PDB 6J5E 6J5E 116 145 DBREF 6J5E I 27 70 UNP Q1HMR5 Q1HMR5_9HIV1 27 70 DBREF 6J5E J 116 145 PDB 6J5E 6J5E 116 145 DBREF 6J5E K 27 70 UNP Q1HMR5 Q1HMR5_9HIV1 27 70 DBREF 6J5E L 116 145 PDB 6J5E 6J5E 116 145 SEQRES 1 G 44 THR VAL GLN ALA ARG GLN LEU LEU SER GLY ILE VAL GLN SEQRES 2 G 44 GLN GLN ASN ASN LEU LEU ARG ALA ILE GLU ALA GLN GLN SEQRES 3 G 44 HIS LEU LEU GLN LEU THR VAL TRP GLY ILE LYS GLN LEU SEQRES 4 G 44 GLN ALA ARG ILE LEU SEQRES 1 H 30 ACE TRP GLU GLU TRP ASP LYS LYS ILE GLU GLU TYR THR SEQRES 2 H 30 LYS LYS ILE GLU GLU LEU ILE LYS LYS SER GLU GLU GLN SEQRES 3 H 30 GLN LYS LYS ASN SEQRES 1 I 44 THR VAL GLN ALA ARG GLN LEU LEU SER GLY ILE VAL GLN SEQRES 2 I 44 GLN GLN ASN ASN LEU LEU ARG ALA ILE GLU ALA GLN GLN SEQRES 3 I 44 HIS LEU LEU GLN LEU THR VAL TRP GLY ILE LYS GLN LEU SEQRES 4 I 44 GLN ALA ARG ILE LEU SEQRES 1 J 30 ACE TRP GLU GLU TRP ASP LYS LYS ILE GLU GLU TYR THR SEQRES 2 J 30 LYS LYS ILE GLU GLU LEU ILE LYS LYS SER GLU GLU GLN SEQRES 3 J 30 GLN LYS LYS ASN SEQRES 1 K 44 THR VAL GLN ALA ARG GLN LEU LEU SER GLY ILE VAL GLN SEQRES 2 K 44 GLN GLN ASN ASN LEU LEU ARG ALA ILE GLU ALA GLN GLN SEQRES 3 K 44 HIS LEU LEU GLN LEU THR VAL TRP GLY ILE LYS GLN LEU SEQRES 4 K 44 GLN ALA ARG ILE LEU SEQRES 1 L 30 ACE TRP GLU GLU TRP ASP LYS LYS ILE GLU GLU TYR THR SEQRES 2 L 30 LYS LYS ILE GLU GLU LEU ILE LYS LYS SER GLU GLU GLN SEQRES 3 L 30 GLN LYS LYS ASN HET ACE H 116 3 HET ACE L 116 3 HETNAM ACE ACETYL GROUP FORMUL 2 ACE 2(C2 H4 O) FORMUL 7 HOH *10(H2 O) HELIX 1 AA1 ALA G 30 ILE G 69 1 40 HELIX 2 AA2 TRP H 117 ASN H 145 1 29 HELIX 3 AA3 LEU I 34 ILE I 69 1 36 HELIX 4 AA4 GLU J 118 LYS J 143 1 26 HELIX 5 AA5 ALA K 30 LEU K 70 1 41 HELIX 6 AA6 TRP L 117 ASN L 145 1 29 LINK C ACE H 116 N TRP H 117 1555 1555 1.33 LINK C ACE L 116 N TRP L 117 1555 1555 1.33 CRYST1 36.500 39.860 171.503 90.00 90.00 90.00 P 21 21 21 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 0.027397 0.000000 0.000000 0.00000 SCALE2 0.000000 0.025088 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005831 0.00000