HEADER UNKNOWN FUNCTION 09-OCT-09 2KP8 TITLE LIGAND BOUND TO A MODEL PEPTIDE THAT MIMICS THE OPEN FUSOGENIC FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: MODEL PEPTIDE; COMPND 3 CHAIN: A, B, C; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PROTEIN/LIGAND, UNKNOWN FUNCTION EXPDTA SOLUTION NMR NUMMDL 5 AUTHOR E.T.OLEJNICZAK REVDAT 3 26-JUL-23 2KP8 1 JRNL REVDAT 2 16-MAR-22 2KP8 1 REMARK REVDAT 1 19-JAN-10 2KP8 0 JRNL AUTH K.D.STEWART,J.R.HUTH,T.I.NG,K.MCDANIEL,R.N.HUTCHINSON, JRNL AUTH 2 V.S.STOLL,R.R.MENDOZA,E.D.MATAYOSHI,R.CARRICK,H.MO, JRNL AUTH 3 J.SEVERIN,K.WALTER,P.L.RICHARDSON,L.W.BARRETT,R.MEADOWS, JRNL AUTH 4 S.ANDERSON,W.KOHLBRENNER,C.MARING,D.J.KEMPF,A.MOLLA, JRNL AUTH 5 E.T.OLEJNICZAK JRNL TITL NON-PEPTIDE ENTRY INHIBITORS OF HIV-1 THAT TARGET THE GP41 JRNL TITL 2 COILED COIL POCKET. JRNL REF BIOORG.MED.CHEM.LETT. V. 20 612 2010 JRNL REFN ESSN 1464-3405 JRNL PMID 20004576 JRNL DOI 10.1016/J.BMCL.2009.11.076 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR, X-PLOR REMARK 3 AUTHORS : BRUNGER, A.T. ET AL. (X-PLOR), BRUNGER, A.T. ET REMARK 3 AL. (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: USING XPLOR, USING SCHRODINGER REMARK 4 REMARK 4 2KP8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-DEC-09. REMARK 100 THE DEPOSITION ID IS D_1000101401. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 318 REMARK 210 PH : 8.0 REMARK 210 IONIC STRENGTH : 25 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM [U-100% 13C; U-100% 15N] REMARK 210 PEPTIDE, 6 MM 3-PYRIDIN-4-YL-2,4-DIHYDRO-INDENO[1,2-.C.]PYRAZOLE, REMARK 210 90% H2O/10% D2O; 1 MM [U-15N]-VLI METHYL13C PEPTIDE, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D CBCA(CO)NH; 3D HNCACB; 3D REMARK 210 HBHA(CO)NH; 3D HCCH-TOCSY; 3D 1H- REMARK 210 15N NOESY; 3D 1H-13C NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TALOS, SCHRODINGER REMARK 210 METHOD USED : SIMULATED ANNEALING, FINAL REMARK 210 MINIMIZATION STEP REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 5 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: EDITED FILTERED NOESY EXPERIMENTS REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 1 GLU C 272 CD GLU C 272 OE1 0.107 REMARK 500 4 GLU C 272 CD GLU C 272 OE1 0.107 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 2 ARG C 245 NE - CZ - NH2 ANGL. DEV. = -3.7 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 1 SER A 2 -137.54 56.41 REMARK 500 1 LEU A 3 -62.27 -91.48 REMARK 500 1 LEU A 25 51.04 -99.33 REMARK 500 1 VAL A 71 -33.85 -130.01 REMARK 500 1 ASP B 126 63.80 -65.04 REMARK 500 1 LEU B 154 48.61 -85.03 REMARK 500 1 GLN B 155 -46.29 -147.11 REMARK 500 1 ASP C 226 87.46 -62.10 REMARK 500 1 GLN C 231 -60.42 70.76 REMARK 500 2 SER A 2 151.67 85.07 REMARK 500 2 LEU A 25 45.95 -94.54 REMARK 500 2 LEU B 123 1.23 -69.00 REMARK 500 2 ASP B 126 64.19 -62.55 REMARK 500 3 SER A 2 151.88 86.79 REMARK 500 3 LEU A 25 31.06 -93.61 REMARK 500 3 SER B 102 -74.54 -35.04 REMARK 500 3 ASP B 126 61.98 -65.77 REMARK 500 3 ASP C 228 -151.31 -168.24 REMARK 500 3 GLN C 231 8.59 -63.66 REMARK 500 4 SER A 2 -63.51 66.50 REMARK 500 4 LEU A 3 -63.62 -161.21 REMARK 500 4 LEU A 25 50.82 -95.52 REMARK 500 4 ASP B 126 63.94 -64.98 REMARK 500 4 LEU C 225 35.26 -148.84 REMARK 500 4 GLN C 231 -60.74 74.76 REMARK 500 5 SER A 2 117.47 78.27 REMARK 500 5 LEU A 25 48.26 -87.26 REMARK 500 5 ASP C 228 -141.13 -145.01 REMARK 500 5 GLN C 231 -55.40 77.36 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 XIG B 999 DBREF 2KP8 A 1 72 PDB 2KP8 2KP8 1 72 DBREF 2KP8 B 101 172 PDB 2KP8 2KP8 101 172 DBREF 2KP8 C 201 272 PDB 2KP8 2KP8 201 272 SEQRES 1 A 72 THR SER LEU ILE HIS SER LEU ILE GLU GLU SER GLN ASN SEQRES 2 A 72 GLN GLN GLU LYS ASN GLU GLN GLU LEU LEU GLU LEU ASP SEQRES 3 A 72 GLY ASP GLY PRO GLN LEU LEU SER GLY ILE VAL GLN GLN SEQRES 4 A 72 GLN ASN ASN LEU LEU ARG ALA ILE GLU ALA GLN GLN HIS SEQRES 5 A 72 LEU LEU GLN LEU THR VAL TRP GLY ILE LYS GLN LEU GLN SEQRES 6 A 72 ALA ARG ILE LEU ALA VAL GLU SEQRES 1 B 72 THR SER LEU ILE HIS SER LEU ILE GLU GLU SER GLN ASN SEQRES 2 B 72 GLN GLN GLU LYS ASN GLU GLN GLU LEU LEU GLU LEU ASP SEQRES 3 B 72 GLY ASP GLY PRO GLN LEU LEU SER GLY ILE VAL GLN GLN SEQRES 4 B 72 GLN ASN ASN LEU LEU ARG ALA ILE GLU ALA GLN GLN HIS SEQRES 5 B 72 LEU LEU GLN LEU THR VAL TRP GLY ILE LYS GLN LEU GLN SEQRES 6 B 72 ALA ARG ILE LEU ALA VAL GLU SEQRES 1 C 72 THR SER LEU ILE HIS SER LEU ILE GLU GLU SER GLN ASN SEQRES 2 C 72 GLN GLN GLU LYS ASN GLU GLN GLU LEU LEU GLU LEU ASP SEQRES 3 C 72 GLY ASP GLY PRO GLN LEU LEU SER GLY ILE VAL GLN GLN SEQRES 4 C 72 GLN ASN ASN LEU LEU ARG ALA ILE GLU ALA GLN GLN HIS SEQRES 5 C 72 LEU LEU GLN LEU THR VAL TRP GLY ILE LYS GLN LEU GLN SEQRES 6 C 72 ALA ARG ILE LEU ALA VAL GLU HET XIG B 999 69 HETNAM XIG 5-{[(4'-METHOXYBIPHENYL-4-YL)METHYL][(1S)-1,2,3,4- HETNAM 2 XIG TETRAHYDRONAPHTHALEN-1-YL]CARBAMOYL}BENZENE-1,2,4- HETNAM 3 XIG TRICARBOXYLIC ACID FORMUL 4 XIG C34 H29 N O8 HELIX 1 1 LEU A 3 LEU A 25 1 23 HELIX 2 2 LEU A 32 LEU A 69 1 38 HELIX 3 3 THR B 101 LEU B 123 1 23 HELIX 4 4 LEU B 132 LEU B 169 1 38 HELIX 5 5 THR C 201 LEU C 225 1 25 HELIX 6 6 LEU C 232 ILE C 268 1 37 HELIX 7 7 LEU C 269 VAL C 271 5 3 SITE 1 AC1 10 LEU A 56 LEU A 64 ARG A 67 THR B 101 SITE 2 AC1 10 SER B 102 LEU B 103 VAL B 158 TRP B 159 SITE 3 AC1 10 LYS B 162 GLN B 165 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1