HEADER VIRAL PROTEIN 17-JUL-15 5CMU TITLE ARTIFICIAL HIV FUSION INHIBITOR AP1 FUSED TO THE C-TERMINUS OF GP41 TITLE 2 NHR COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENVELOPE GLYCOPROTEIN,AP1; COMPND 3 CHAIN: A, B, C; COMPND 4 FRAGMENT: C-TERMINUS (UNP RESIDUES 35-70); COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: THE FUSION PROTEIN OF EXPRESSION TAG, C-TERMINUS COMPND 7 RESIDUES 35-70 FROM GP4 AND ARTIFICIAL INHIBITOR AP1 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1, SYNTHETIC SOURCE 3 CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 11676, 32630; SOURCE 5 GENE: ENV; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ENFUVIRTIDE, HIV FUSION INHIBITOR, AP1, GP41, 6-HB, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.ZHU,S.YE,R.ZHANG REVDAT 2 20-MAR-24 5CMU 1 REMARK REVDAT 1 16-SEP-15 5CMU 0 JRNL AUTH X.ZHU,Y.ZHU,S.YE,Q.WANG,W.XU,S.SU,Z.SUN,F.YU,Q.LIU,C.WANG, JRNL AUTH 2 T.ZHANG,Z.ZHANG,X.ZHANG,J.XU,L.DU,K.LIU,L.LU,R.ZHANG,S.JIANG JRNL TITL IMPROVED PHARMACOLOGICAL AND STRUCTURAL PROPERTIES OF HIV JRNL TITL 2 FUSION INHIBITOR AP3 OVER ENFUVIRTIDE: HIGHLIGHTING JRNL TITL 3 ADVANTAGES OF ARTIFICIAL PEPTIDE STRATEGY. JRNL REF SCI REP V. 5 13028 2015 JRNL REFN ESSN 2045-2322 JRNL PMID 26286358 JRNL DOI 10.1038/SREP13028 REMARK 2 REMARK 2 RESOLUTION. 2.11 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.2_1309 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) : 2.11 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.03 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.6 REMARK 3 NUMBER OF REFLECTIONS : 11528 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.215 REMARK 3 R VALUE (WORKING SET) : 0.212 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.890 REMARK 3 FREE R VALUE TEST SET COUNT : 1140 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 10.0000 - 4.2232 0.94 1371 152 0.2273 0.2426 REMARK 3 2 4.2232 - 3.3533 0.99 1407 163 0.1781 0.2129 REMARK 3 3 3.3533 - 2.9298 1.00 1407 160 0.2205 0.2812 REMARK 3 4 2.9298 - 2.6621 1.00 1421 148 0.2300 0.2580 REMARK 3 5 2.6621 - 2.4714 0.99 1394 156 0.2137 0.2413 REMARK 3 6 2.4714 - 2.3257 0.92 1305 141 0.2018 0.2455 REMARK 3 7 2.3257 - 2.2093 0.74 1070 107 0.2357 0.2545 REMARK 3 8 2.2093 - 2.1131 0.73 1013 113 0.2083 0.2447 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) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.900 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 1828 REMARK 3 ANGLE : 0.838 2433 REMARK 3 CHIRALITY : 0.055 262 REMARK 3 PLANARITY : 0.002 307 REMARK 3 DIHEDRAL : 20.361 726 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 5CMU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 23-JUL-15. REMARK 100 THE DEPOSITION ID IS D_1000211883. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-AUG-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97937 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 : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 31.030 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.9000 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: NULL 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 (%): 43.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS-HCL PH 8.5, 32% (W/V) PEG REMARK 280 3350, 0.2M MGCL2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 29.40550 REMARK 290 SMTRY3 2 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 8570 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11760 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -68.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 SER B 0 REMARK 465 SER C 0 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 A 201 O HOH A 210 1.86 REMARK 500 O HOH C 216 O HOH C 217 1.91 REMARK 500 O LEU C 36 O HOH C 201 1.98 REMARK 500 O3 GOL C 101 O HOH C 202 2.02 REMARK 500 O HOH C 203 O HOH C 221 2.06 REMARK 500 O SER C 1 O HOH C 203 2.10 REMARK 500 NZ LYS C 29 O HOH C 204 2.18 REMARK 500 NE2 GLN B 22 O HOH B 201 2.18 REMARK 500 N GLY B 42 O2 GOL B 101 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O SER B 1 OG SER C 37 1556 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL C 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL C 102 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5CMZ RELATED DB: PDB REMARK 900 RELATED ID: 5CN0 RELATED DB: PDB DBREF 5CMU A 1 36 UNP Q1HMR5 Q1HMR5_9HIV1 35 70 DBREF 5CMU A 37 72 PDB 5CMU 5CMU 37 72 DBREF 5CMU B 1 36 UNP Q1HMR5 Q1HMR5_9HIV1 35 70 DBREF 5CMU B 37 72 PDB 5CMU 5CMU 37 72 DBREF 5CMU C 1 36 UNP Q1HMR5 Q1HMR5_9HIV1 35 70 DBREF 5CMU C 37 72 PDB 5CMU 5CMU 37 72 SEQADV 5CMU SER A 0 UNP Q1HMR5 EXPRESSION TAG SEQADV 5CMU SER B 0 UNP Q1HMR5 EXPRESSION TAG SEQADV 5CMU SER C 0 UNP Q1HMR5 EXPRESSION TAG SEQRES 1 A 73 SER SER GLY ILE VAL GLN GLN GLN ASN ASN LEU LEU ARG SEQRES 2 A 73 ALA ILE GLU ALA GLN GLN HIS LEU LEU GLN LEU THR VAL SEQRES 3 A 73 TRP GLY ILE LYS GLN LEU GLN ALA ARG ILE LEU SER GLY SEQRES 4 A 73 GLY ARG GLY GLY TRP MET GLU TRP ASP ARG GLU ILE GLU SEQRES 5 A 73 GLU LEU ILE LYS LYS SER GLU GLU LEU ILE LYS LYS ILE SEQRES 6 A 73 GLU GLU GLN ILE LYS LYS GLN GLU SEQRES 1 B 73 SER SER GLY ILE VAL GLN GLN GLN ASN ASN LEU LEU ARG SEQRES 2 B 73 ALA ILE GLU ALA GLN GLN HIS LEU LEU GLN LEU THR VAL SEQRES 3 B 73 TRP GLY ILE LYS GLN LEU GLN ALA ARG ILE LEU SER GLY SEQRES 4 B 73 GLY ARG GLY GLY TRP MET GLU TRP ASP ARG GLU ILE GLU SEQRES 5 B 73 GLU LEU ILE LYS LYS SER GLU GLU LEU ILE LYS LYS ILE SEQRES 6 B 73 GLU GLU GLN ILE LYS LYS GLN GLU SEQRES 1 C 73 SER SER GLY ILE VAL GLN GLN GLN ASN ASN LEU LEU ARG SEQRES 2 C 73 ALA ILE GLU ALA GLN GLN HIS LEU LEU GLN LEU THR VAL SEQRES 3 C 73 TRP GLY ILE LYS GLN LEU GLN ALA ARG ILE LEU SER GLY SEQRES 4 C 73 GLY ARG GLY GLY TRP MET GLU TRP ASP ARG GLU ILE GLU SEQRES 5 C 73 GLU LEU ILE LYS LYS SER GLU GLU LEU ILE LYS LYS ILE SEQRES 6 C 73 GLU GLU GLN ILE LYS LYS GLN GLU HET GOL A 101 6 HET GOL B 101 6 HET GOL B 102 6 HET GOL C 101 6 HET GOL C 102 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 4 GOL 5(C3 H8 O3) FORMUL 9 HOH *71(H2 O) HELIX 1 AA1 GLY A 2 LEU A 36 1 35 HELIX 2 AA2 GLY A 42 LYS A 70 1 29 HELIX 3 AA3 GLY B 2 LEU B 36 1 35 HELIX 4 AA4 GLY B 39 GLY B 41 5 3 HELIX 5 AA5 GLY B 42 GLN B 71 1 30 HELIX 6 AA6 GLY C 2 LEU C 36 1 35 HELIX 7 AA7 GLY C 39 GLY C 41 5 3 HELIX 8 AA8 GLY C 42 GLU C 72 1 31 SITE 1 AC1 5 GLY A 42 TRP A 46 GLU A 49 LEU C 23 SITE 2 AC1 5 TRP C 26 SITE 1 AC2 7 GLY B 39 ARG B 40 GLY B 41 GLY B 42 SITE 2 AC2 7 TRP B 43 MET B 44 GLU B 45 SITE 1 AC3 5 GLN B 30 ARG B 34 LEU C 36 GLY C 41 SITE 2 AC3 5 TRP C 43 SITE 1 AC4 5 LYS C 62 LYS C 63 GLU C 66 HOH C 202 SITE 2 AC4 5 HOH C 214 SITE 1 AC5 4 LYS C 29 GLN C 32 ASP C 47 HOH C 213 CRYST1 36.617 58.811 51.439 90.00 93.97 90.00 P 1 21 1 6 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 0.027310 0.000000 0.001896 0.00000 SCALE2 0.000000 0.017004 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019487 0.00000