1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Demene, H. Morellet, N. Teilleux, V. Huynh-Dinh, T. De Rocquigny, H. Fournie-Zaluski, M.C. Roques, B.P. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 1 90.00 90.00 90.00 1.000 1.000 1.000 C3 H7 N O2 89.093 y ALANINE L-peptide linking C6 H15 N4 O2 1 175.209 y ARGININE L-peptide linking C4 H8 N2 O3 132.118 y ASPARAGINE L-peptide linking C4 H7 N O4 133.103 y ASPARTIC ACID L-peptide linking C3 H7 N O2 S 121.158 y CYSTEINE L-peptide linking C10 H14 N5 O6 P 331.222 y 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE DNA linking C9 H14 N3 O7 P 307.197 y 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE DNA linking C10 H14 N5 O7 P 347.221 y 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE DNA linking C5 H10 N2 O3 146.144 y GLUTAMINE L-peptide linking C5 H9 N O4 147.129 y GLUTAMIC ACID L-peptide linking C2 H5 N O2 75.067 y GLYCINE peptide linking C6 H10 N3 O2 1 156.162 y HISTIDINE L-peptide linking C6 H15 N2 O2 1 147.195 y LYSINE L-peptide linking C5 H11 N O2 S 149.211 y METHIONINE L-peptide linking C9 H11 N O2 165.189 y PHENYLALANINE L-peptide linking C5 H9 N O2 115.130 y PROLINE L-peptide linking C4 H9 N O3 119.119 y THREONINE L-peptide linking C11 H12 N2 O2 204.225 y TRYPTOPHAN L-peptide linking C5 H11 N O2 117.146 y VALINE L-peptide linking Zn 2 65.409 ZINC ION non-polymer UK J.Mol.Biol. JMOBAK 0070 0022-2836 283 419 434 10.1006/jmbi.1998.2098 9769215 Structure of the complex between the HIV-1 nucleocapsid protein NCp7 and the single-stranded pentanucleotide d(ACGCC). 1998 10.2210/pdb1bj6/pdb pdb_00001bj6 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 1465.001 DNA (5'-D(*AP*CP*GP*CP*C)-3') 1 syn polymer 4837.642 NUCLEOCAPSID PROTEIN 7 RESIDUES 12-53 1 man polymer 65.409 ZINC ION 2 syn non-polymer (12-53)NCP7 no no (DA)(DC)(DG)(DC)(DC) ACGCC D polydeoxyribonucleotide no no NVKCFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCTERQ NVKCFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCTERQ A polypeptide(L) n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n Lentivirus MAL sample 11676 Human immunodeficiency virus 1 database_2 pdbx_database_status pdbx_nmr_software pdbx_struct_assembly pdbx_struct_oper_list struct_conn struct_site repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations Other 1 0 1999-02-02 1 1 2008-03-24 1 2 2011-07-13 1 3 2022-02-16 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_database_status.process_site _pdbx_nmr_software.name _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_auth_seq_id Y BNL 1998-07-03 REL ZN ZINC ION LEAST RESTRAINT VIOLATION AND LOWEST TOTAL ENERGY 50 10 NOESY TOCSY DQF LOW SALT CONDITIONS 6.0 1 atm 303 K THE PROTEIN PART OF THE STRUCTURE WAS FIRST GENERATED USING A RESTRAINTED DYNAMICAL ANNEALING CALCULATION. THE D(ACGCC) NUCLEIC ACID UNDER A DNA CONFORMATION WAS DOCKED APPROXIMATIVELY TO THE PROTEIN BASED ON THE 28 INTERMOLECULAR NOES. THE DOCKED STRUCTURE WAS ENERGY-MINIMIZED UNDER NOES RESTRAINTS. THIS INITIAL COMPLEXED STRUCTURE WAS THEN USED FOR A SECOND SET OF SIMULATED ANNEALING CALCULATION. DYNAMICAL SIMULATED ANNEALING WATER BIOSYM refinement Discover structure solution BRUKER DISNMR DISNMR structure solution BIOSYM/MSI 600 Bruker AMX600 ZN 54 3 ZN H ZN 54 A ZN 55 3 ZN H ZN 55 A A 1 n 1 DA 1 D C 2 n 2 DC 2 D G 3 n 3 DG 3 D C 4 n 4 DC 4 D C 5 n 5 DC 5 D ASN 12 n 1 ASN 12 A VAL 13 n 2 VAL 13 A LYS 14 n 3 LYS 14 A CYS 15 n 4 CYS 15 A PHE 16 n 5 PHE 16 A ASN 17 n 6 ASN 17 A CYS 18 n 7 CYS 18 A GLY 19 n 8 GLY 19 A LYS 20 n 9 LYS 20 A GLU 21 n 10 GLU 21 A GLY 22 n 11 GLY 22 A HIS 23 n 12 HIS 23 A THR 24 n 13 THR 24 A ALA 25 n 14 ALA 25 A ARG 26 n 15 ARG 26 A ASN 27 n 16 ASN 27 A CYS 28 n 17 CYS 28 A ARG 29 n 18 ARG 29 A ALA 30 n 19 ALA 30 A PRO 31 n 20 PRO 31 A ARG 32 n 21 ARG 32 A LYS 33 n 22 LYS 33 A LYS 34 n 23 LYS 34 A GLY 35 n 24 GLY 35 A CYS 36 n 25 CYS 36 A TRP 37 n 26 TRP 37 A LYS 38 n 27 LYS 38 A CYS 39 n 28 CYS 39 A GLY 40 n 29 GLY 40 A LYS 41 n 30 LYS 41 A GLU 42 n 31 GLU 42 A GLY 43 n 32 GLY 43 A HIS 44 n 33 HIS 44 A GLN 45 n 34 GLN 45 A MET 46 n 35 MET 46 A LYS 47 n 36 LYS 47 A ASP 48 n 37 ASP 48 A CYS 49 n 38 CYS 49 A THR 50 n 39 THR 50 A GLU 51 n 40 GLU 51 A ARG 52 n 41 ARG 52 A GLN 53 n 42 GLN 53 A author_defined_assembly 2 dimeric A CYS 15 B SG CYS 4 1_555 H A ZN 54 C ZN ZN 1_555 A CYS 18 B SG CYS 7 1_555 114.9 A CYS 15 B SG CYS 4 1_555 H A ZN 54 C ZN ZN 1_555 A HIS 23 B NE2 HIS 12 1_555 105.4 A CYS 18 B SG CYS 7 1_555 H A ZN 54 C ZN ZN 1_555 A HIS 23 B NE2 HIS 12 1_555 109.4 A CYS 15 B SG CYS 4 1_555 H A ZN 54 C ZN ZN 1_555 A CYS 28 B SG CYS 17 1_555 109.9 A CYS 18 B SG CYS 7 1_555 H A ZN 54 C ZN ZN 1_555 A CYS 28 B SG CYS 17 1_555 107.9 A HIS 23 B NE2 HIS 12 1_555 H A ZN 54 C ZN ZN 1_555 A CYS 28 B SG CYS 17 1_555 109.2 A CYS 36 B SG CYS 25 1_555 H A ZN 55 D ZN ZN 1_555 A CYS 39 B SG CYS 28 1_555 113.9 A CYS 36 B SG CYS 25 1_555 H A ZN 55 D ZN ZN 1_555 A HIS 44 B NE2 HIS 33 1_555 106.0 A CYS 39 B SG CYS 28 1_555 H A ZN 55 D ZN ZN 1_555 A HIS 44 B NE2 HIS 33 1_555 108.0 A CYS 36 B SG CYS 25 1_555 H A ZN 55 D ZN ZN 1_555 A CYS 49 B SG CYS 38 1_555 106.8 A CYS 39 B SG CYS 28 1_555 H A ZN 55 D ZN ZN 1_555 A CYS 49 B SG CYS 38 1_555 112.4 A HIS 44 B NE2 HIS 33 1_555 H A ZN 55 D ZN ZN 1_555 A CYS 49 B SG CYS 38 1_555 109.4 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 x,y,z identity operation 0.0000000000 0.0000000000 0.0000000000 1 D DG 3 0.062 SIDE CHAIN 5 D DC 2 0.094 SIDE CHAIN 8 D DC 2 0.091 SIDE CHAIN 9 D DC 5 0.074 SIDE CHAIN 10 A ARG 52 0.090 SIDE CHAIN 1 3.86 0.60 118.90 122.76 D D D N1 C2 O2 DC DC DC 2 2 2 N 1 2.78 0.30 108.30 111.08 D D D O4' C1' N1 DC DC DC 4 4 4 N 2 -5.08 0.70 102.20 97.12 D D D C4' C3' C2' DA DA DA 1 1 1 N 2 3.09 0.30 108.30 111.39 D D D O4' C1' N9 DA DA DA 1 1 1 N 2 3.08 0.30 108.30 111.38 D D D O4' C1' N1 DC DC DC 4 4 4 N 3 2.65 0.30 108.30 110.95 D D D O4' C1' N1 DC DC DC 2 2 2 N 3 3.37 0.30 108.30 111.67 D D D O4' C1' N1 DC DC DC 4 4 4 N 3 2.63 0.30 108.30 110.93 D D D O4' C1' N1 DC DC DC 5 5 5 N 4 3.70 0.30 108.30 112.00 D D D O4' C1' N9 DA DA DA 1 1 1 N 4 3.66 0.30 108.30 111.96 D D D O4' C1' N1 DC DC DC 2 2 2 N 4 4.37 0.30 108.30 112.67 D D D O4' C1' N1 DC DC DC 4 4 4 N 4 3.07 0.30 108.30 111.37 D D D O4' C1' N1 DC DC DC 5 5 5 N 5 3.77 0.30 108.30 112.07 D D D O4' C1' N1 DC DC DC 4 4 4 N 6 2.30 0.30 108.30 110.60 D D D O4' C1' N1 DC DC DC 2 2 2 N 6 4.54 0.30 108.30 112.84 D D D O4' C1' N1 DC DC DC 4 4 4 N 6 3.88 0.30 108.30 112.18 D D D O4' C1' N1 DC DC DC 5 5 5 N 7 -4.34 0.70 102.20 97.86 D D D C4' C3' C2' DA DA DA 1 1 1 N 7 4.29 0.30 108.30 112.59 D D D O4' C1' N9 DA DA DA 1 1 1 N 7 4.01 0.60 118.90 122.91 D D D N1 C2 O2 DC DC DC 2 2 2 N 7 2.47 0.30 108.30 110.77 D D D O4' C1' N1 DC DC DC 4 4 4 N 7 2.30 0.30 108.30 110.60 D D D O4' C1' N1 DC DC DC 5 5 5 N 8 5.95 0.30 108.30 114.25 D D D O4' C1' N9 DA DA DA 1 1 1 N 8 4.53 0.30 108.30 112.83 D D D O4' C1' N1 DC DC DC 2 2 2 N 8 3.80 0.30 108.30 112.10 D D D O4' C1' N1 DC DC DC 4 4 4 N 8 2.41 0.30 108.30 110.71 D D D O4' C1' N1 DC DC DC 5 5 5 N 9 3.96 0.30 108.30 112.26 D D D O4' C1' N9 DA DA DA 1 1 1 N 9 4.42 0.30 108.30 112.72 D D D O4' C1' N1 DC DC DC 4 4 4 N 9 3.45 0.30 108.30 111.75 D D D O4' C1' N1 DC DC DC 5 5 5 N 10 -4.62 0.70 102.20 97.58 D D D C4' C3' C2' DA DA DA 1 1 1 N 10 3.90 0.30 108.30 112.20 D D D O4' C1' N9 DA DA DA 1 1 1 N 10 2.19 0.30 108.30 110.49 D D D O4' C1' N1 DC DC DC 4 4 4 N 1 A ASN 17 -143.86 -85.72 1 A THR 50 -161.23 28.65 2 A CYS 15 -33.96 117.55 2 A ASN 17 -82.29 -88.64 2 A THR 50 -172.92 40.68 2 A GLU 51 -14.51 -81.19 3 A LYS 14 -163.23 67.84 3 A CYS 15 -0.79 111.70 3 A ASN 17 -155.66 -64.58 3 A HIS 44 -160.04 -161.19 3 A THR 50 -179.33 37.32 3 A GLU 51 -17.62 -78.97 3 A ARG 52 29.50 40.55 4 A ASN 17 -75.05 -77.67 4 A LYS 38 -56.19 -76.43 4 A THR 50 -165.18 29.80 4 A ARG 52 25.12 67.85 5 A VAL 13 -139.07 -57.21 5 A LYS 14 76.92 105.20 5 A PHE 16 -79.62 48.99 5 A ASN 17 -151.54 -74.27 5 A LYS 38 -56.15 -71.83 5 A HIS 44 -103.60 -160.84 5 A THR 50 -177.15 36.22 5 A GLU 51 -22.36 -76.29 5 A ARG 52 56.40 74.27 6 A CYS 15 -28.88 121.74 6 A PHE 16 -83.92 49.25 6 A ASN 17 -152.33 -77.47 6 A HIS 44 -97.03 -148.58 6 A THR 50 -160.90 38.04 6 A ARG 52 -66.60 -152.65 7 A PHE 16 -91.44 39.21 7 A ASN 17 -148.06 -75.41 7 A THR 50 -152.14 25.47 7 A GLU 51 -91.45 -120.10 7 A ARG 52 156.21 134.69 8 A ASN 17 -149.44 -80.14 8 A THR 50 -177.99 36.70 8 A GLU 51 -7.06 -80.12 9 A CYS 15 -34.95 124.00 9 A ASN 17 -154.88 -83.80 9 A THR 50 -141.97 19.07 9 A ARG 52 -163.77 85.87 10 A CYS 15 -21.44 114.95 10 A ASN 17 -151.95 -73.79 10 A LYS 38 -57.14 -74.14 10 A HIS 44 -116.76 -162.78 10 A ARG 52 -169.22 79.12 1H NMR OF (12-53) NCP7/D(ACGCC) COMPLEX, 10 STRUCTURES 1 N N 2 N N 3 N N 3 N N metalc 2.312 H A CYS 15 B SG CYS 4 1_555 A ZN 54 C ZN ZN 1_555 metalc 2.255 H A CYS 18 B SG CYS 7 1_555 A ZN 54 C ZN ZN 1_555 metalc 2.037 H A HIS 23 B NE2 HIS 12 1_555 A ZN 54 C ZN ZN 1_555 metalc 2.229 H A CYS 28 B SG CYS 17 1_555 A ZN 54 C ZN ZN 1_555 metalc 2.303 H A CYS 36 B SG CYS 25 1_555 A ZN 55 D ZN ZN 1_555 metalc 2.266 H A CYS 39 B SG CYS 28 1_555 A ZN 55 D ZN ZN 1_555 metalc 2.025 H A HIS 44 B NE2 HIS 33 1_555 A ZN 55 D ZN ZN 1_555 metalc 2.267 H A CYS 49 B SG CYS 38 1_555 A ZN 55 D ZN ZN 1_555 Viral protein/DNA COMPLEX (NUCLEOCAPSID PROTEIN-DNA), NUCLEIC ACID, RETROVIRUS, VIRUS MORPHOGENESIS, ZINC FINGER, Viral protein-DNA COMPLEX Q74084_9HIV1 UNP 2 390 Q74084 1BJ6 PDB 1 1BJ6 390 430 1BJ6 13 53 Q74084 A 1 2 42 1 5 1BJ6 1 5 1BJ6 D 2 1 5 ZINC-BINDING SITES. Unknown 7 BINDING SITE FOR RESIDUE ZN A 54H A ZN H 54 Software 4 BINDING SITE FOR RESIDUE ZN A 55H A ZN H 55 Software 4 A CYS 15 B CYS 4 7 1_555 A CYS 18 B CYS 7 7 1_555 A HIS 23 B HIS 12 7 1_555 A CYS 28 B CYS 17 7 1_555 A CYS 36 B CYS 25 7 1_555 A CYS 39 B CYS 28 7 1_555 A HIS 44 B HIS 33 7 1_555 A CYS 15 B CYS 4 4 1_555 A CYS 18 B CYS 7 4 1_555 A HIS 23 B HIS 12 4 1_555 A CYS 28 B CYS 17 4 1_555 A CYS 36 B CYS 25 4 1_555 A CYS 39 B CYS 28 4 1_555 A HIS 44 B HIS 33 4 1_555 A CYS 49 B CYS 38 4 1_555 1 P 1