1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 South, T.L. Summers, M.F. 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 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 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 H13 N O2 131.173 y ISOLEUCINE L-peptide linking C6 H15 N2 O2 1 147.195 y LYSINE L-peptide linking C9 H11 N O2 165.189 y PHENYLALANINE L-peptide linking C5 H11 N O2 117.146 y VALINE L-peptide linking Zn 2 65.409 ZINC ION non-polymer US Protein Sci. PRCIEI 0795 0961-8368 2 3 8443588 Zinc- and sequence-dependent binding to nucleic acids by the N-terminal zinc finger of the HIV-1 nucleocapsid protein: NMR structure of the complex with the Psi-site analog, dACGCC. 1993 US Protein Sci. PRCIEI 0795 0961-8368 1 563 Nucleocapsid Zinc Fingers Detected in Retroviruses: Exafs Studies of Intact Viruses and the Solution-State Structure of the Nucleocapsid Protein from HIV-1 1992 US Biochemistry BICHAW 0033 0006-2960 30 6342 The C-Terminal Retroviral-Type Zinc Finger Domain from the HIV-1 Nucleocapsid Protein is Structurally Similar to the N-Terminal Zinc Finger Domain 1991 US Biochemistry BICHAW 0033 0006-2960 29 7786 The Nucleocapsid Protein Isolated from HIV-I Particles Binds Zinc and Form Retroviral-Type Zinc Fingers 1990 10.2210/pdb1hvo/pdb pdb_00001hvo 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(P*AP*CP*GP*CP*C)-3') 1 syn polymer 2011.379 Hiv-1 Nucleocapsid Zinc Finger 1 man polymer 65.409 ZINC ION 1 syn non-polymer DEOXYRIBONUCLEIC ACID POLYPEPTIDE no no (DA)(DC)(DG)(DC)(DC) ACGCC D polydeoxyribonucleotide no no VKCFNCGKEGHIARNCRA VKCFNCGKEGHIARNCRA E 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 Lentivirus sample 11676 Human immunodeficiency virus 1 database_2 pdbx_database_status pdbx_struct_assembly pdbx_struct_oper_list struct_conn struct_site repository Initial release Version format compliance Version format compliance Database references Derived calculations Other 1 0 1994-01-31 1 1 2008-03-24 1 2 2011-07-13 1 3 2022-02-23 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_database_status.process_site _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_seq_id Y BNL 1992-12-08 REL ZN ZINC ION THE AVERAGE PAIRWISE RMDS'S FOR THE 40 DG/SA STRUCTURES (C,CA,N ATOMS OF RESIDUES A1-L51) IS 0.42 (0.07) ANGSTROMS. THE AVERAGE RMS DEVIATION FOR THE 40 DG/SA STRUCTURES RELATIVE TO THE MEAN COORDINATES (C,CA,N ATOMS OF RESIDUES A1-L51) IS 0.29 (0.07) ANGSTROMS. 15 THE INTERNAL CONFORMATION OF THE OLIGODEOXYRIBONUCLEOTIDE, D(ACGCC), WAS HELD FIXED IN AN IDEALIZED A-HELICAL CONFORMATION. THE A-HELIX STRUCTURE WAS GENERATED WITH QUANTA. SIMULATED ANNEALING WAS PERFORMED IN A MANNER THAT ALLOWED ATOMS OF THE ZINC FINGER ONLY TO MOVE DURING REFINEMENT. simulated annealing refinement DSPACE ZN 19 3 ZN ZN 19 E 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 VAL 1 n 1 VAL 1 E LYS 2 n 2 LYS 2 E CYS 3 n 3 CYS 3 E PHE 4 n 4 PHE 4 E ASN 5 n 5 ASN 5 E CYS 6 n 6 CYS 6 E GLY 7 n 7 GLY 7 E LYS 8 n 8 LYS 8 E GLU 9 n 9 GLU 9 E GLY 10 n 10 GLY 10 E HIS 11 n 11 HIS 11 E ILE 12 n 12 ILE 12 E ALA 13 n 13 ALA 13 E ARG 14 n 14 ARG 14 E ASN 15 n 15 ASN 15 E CYS 16 n 16 CYS 16 E ARG 17 n 17 ARG 17 E ALA 18 n 18 ALA 18 E author_defined_assembly 2 dimeric E CYS 3 B SG CYS 3 1_555 E ZN 19 C ZN ZN 1_555 E CYS 6 B SG CYS 6 1_555 106.7 E CYS 3 B SG CYS 3 1_555 E ZN 19 C ZN ZN 1_555 E HIS 11 B NE2 HIS 11 1_555 92.8 E CYS 6 B SG CYS 6 1_555 E ZN 19 C ZN ZN 1_555 E HIS 11 B NE2 HIS 11 1_555 99.6 E CYS 3 B SG CYS 3 1_555 E ZN 19 C ZN ZN 1_555 E CYS 16 B SG CYS 16 1_555 124.4 E CYS 6 B SG CYS 6 1_555 E ZN 19 C ZN ZN 1_555 E CYS 16 B SG CYS 16 1_555 108.2 E HIS 11 B NE2 HIS 11 1_555 E ZN 19 C ZN ZN 1_555 E CYS 16 B SG CYS 16 1_555 121.8 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 E LYS 2 -10.86 1 E CYS 3 -11.55 2 E LYS 2 -10.28 2 E ILE 12 -10.81 3 E LYS 2 -10.32 4 E VAL 1 -10.23 4 E LYS 2 -10.36 5 E CYS 3 -10.33 5 E ARG 14 10.78 6 E LYS 2 -11.27 7 E CYS 3 -11.68 8 E CYS 3 -10.73 9 E CYS 3 -10.72 9 E ASN 5 -11.82 10 E CYS 3 -11.48 11 E CYS 3 -10.86 11 E ASN 15 10.25 12 E CYS 3 -12.76 13 E CYS 3 -10.91 14 E LYS 2 -10.57 14 E CYS 3 -10.71 14 E ILE 12 -10.19 15 E CYS 3 -12.24 1 -11.92 1.20 119.70 107.78 D D D C3' O3' P DA DA DC 1 1 2 Y 1 -12.02 1.20 119.70 107.68 D D D C3' O3' P DC DC DG 2 2 3 Y 1 -11.88 1.20 119.70 107.82 D D D C3' O3' P DG DG DC 3 3 4 Y 1 1.88 0.30 108.30 110.18 D D D O4' C1' N1 DC DC DC 4 4 4 N 1 -11.24 1.20 119.70 108.46 D D D C3' O3' P DC DC DC 4 4 5 Y 1 2.03 0.30 108.30 110.33 D D D O4' C1' N1 DC DC DC 5 5 5 N 2 -11.93 1.20 119.70 107.77 D D D C3' O3' P DA DA DC 1 1 2 Y 2 -12.01 1.20 119.70 107.69 D D D C3' O3' P DC DC DG 2 2 3 Y 2 -11.84 1.20 119.70 107.86 D D D C3' O3' P DG DG DC 3 3 4 Y 2 1.91 0.30 108.30 110.21 D D D O4' C1' N1 DC DC DC 4 4 4 N 2 -11.27 1.20 119.70 108.43 D D D C3' O3' P DC DC DC 4 4 5 Y 2 2.04 0.30 108.30 110.34 D D D O4' C1' N1 DC DC DC 5 5 5 N 3 -11.92 1.20 119.70 107.78 D D D C3' O3' P DA DA DC 1 1 2 Y 3 -12.02 1.20 119.70 107.68 D D D C3' O3' P DC DC DG 2 2 3 Y 3 -11.88 1.20 119.70 107.82 D D D C3' O3' P DG DG DC 3 3 4 Y 3 1.89 0.30 108.30 110.19 D D D O4' C1' N1 DC DC DC 4 4 4 N 3 -11.25 1.20 119.70 108.45 D D D C3' O3' P DC DC DC 4 4 5 Y 3 2.02 0.30 108.30 110.32 D D D O4' C1' N1 DC DC DC 5 5 5 N 4 -11.94 1.20 119.70 107.76 D D D C3' O3' P DA DA DC 1 1 2 Y 4 -11.99 1.20 119.70 107.71 D D D C3' O3' P DC DC DG 2 2 3 Y 4 -11.83 1.20 119.70 107.87 D D D C3' O3' P DG DG DC 3 3 4 Y 4 1.85 0.30 108.30 110.15 D D D O4' C1' N1 DC DC DC 4 4 4 N 4 -11.29 1.20 119.70 108.41 D D D C3' O3' P DC DC DC 4 4 5 Y 4 2.02 0.30 108.30 110.32 D D D O4' C1' N1 DC DC DC 5 5 5 N 5 -11.93 1.20 119.70 107.77 D D D C3' O3' P DA DA DC 1 1 2 Y 5 -12.01 1.20 119.70 107.69 D D D C3' O3' P DC DC DG 2 2 3 Y 5 -11.90 1.20 119.70 107.80 D D D C3' O3' P DG DG DC 3 3 4 Y 5 1.85 0.30 108.30 110.15 D D D O4' C1' N1 DC DC DC 4 4 4 N 5 -11.26 1.20 119.70 108.44 D D D C3' O3' P DC DC DC 4 4 5 Y 5 2.03 0.30 108.30 110.33 D D D O4' C1' N1 DC DC DC 5 5 5 N 6 -11.92 1.20 119.70 107.78 D D D C3' O3' P DA DA DC 1 1 2 Y 6 -12.06 1.20 119.70 107.64 D D D C3' O3' P DC DC DG 2 2 3 Y 6 -11.91 1.20 119.70 107.79 D D D C3' O3' P DG DG DC 3 3 4 Y 6 1.84 0.30 108.30 110.14 D D D O4' C1' N1 DC DC DC 4 4 4 N 6 -11.24 1.20 119.70 108.46 D D D C3' O3' P DC DC DC 4 4 5 Y 6 2.03 0.30 108.30 110.33 D D D O4' C1' N1 DC DC DC 5 5 5 N 7 -11.95 1.20 119.70 107.75 D D D C3' O3' P DA DA DC 1 1 2 Y 7 -12.03 1.20 119.70 107.67 D D D C3' O3' P DC DC DG 2 2 3 Y 7 -11.88 1.20 119.70 107.82 D D D C3' O3' P DG DG DC 3 3 4 Y 7 1.87 0.30 108.30 110.17 D D D O4' C1' N1 DC DC DC 4 4 4 N 7 -11.22 1.20 119.70 108.48 D D D C3' O3' P DC DC DC 4 4 5 Y 7 2.04 0.30 108.30 110.34 D D D O4' C1' N1 DC DC DC 5 5 5 N 8 -11.92 1.20 119.70 107.78 D D D C3' O3' P DA DA DC 1 1 2 Y 8 -11.99 1.20 119.70 107.71 D D D C3' O3' P DC DC DG 2 2 3 Y 8 -11.88 1.20 119.70 107.82 D D D C3' O3' P DG DG DC 3 3 4 Y 8 1.92 0.30 108.30 110.22 D D D O4' C1' N1 DC DC DC 4 4 4 N 8 -11.22 1.20 119.70 108.48 D D D C3' O3' P DC DC DC 4 4 5 Y 8 2.04 0.30 108.30 110.34 D D D O4' C1' N1 DC DC DC 5 5 5 N 9 -11.88 1.20 119.70 107.82 D D D C3' O3' P DA DA DC 1 1 2 Y 9 -12.04 1.20 119.70 107.66 D D D C3' O3' P DC DC DG 2 2 3 Y 9 -11.85 1.20 119.70 107.85 D D D C3' O3' P DG DG DC 3 3 4 Y 9 1.91 0.30 108.30 110.21 D D D O4' C1' N1 DC DC DC 4 4 4 N 9 -11.21 1.20 119.70 108.49 D D D C3' O3' P DC DC DC 4 4 5 Y 9 2.01 0.30 108.30 110.31 D D D O4' C1' N1 DC DC DC 5 5 5 N 9 -4.30 0.70 120.80 116.50 E E E CB CG CD2 PHE PHE PHE 4 4 4 N 10 -11.91 1.20 119.70 107.79 D D D C3' O3' P DA DA DC 1 1 2 Y 10 -12.03 1.20 119.70 107.67 D D D C3' O3' P DC DC DG 2 2 3 Y 10 -11.86 1.20 119.70 107.84 D D D C3' O3' P DG DG DC 3 3 4 Y 10 1.90 0.30 108.30 110.20 D D D O4' C1' N1 DC DC DC 4 4 4 N 10 -11.20 1.20 119.70 108.50 D D D C3' O3' P DC DC DC 4 4 5 Y 10 2.00 0.30 108.30 110.30 D D D O4' C1' N1 DC DC DC 5 5 5 N 11 -11.95 1.20 119.70 107.75 D D D C3' O3' P DA DA DC 1 1 2 Y 11 -12.04 1.20 119.70 107.66 D D D C3' O3' P DC DC DG 2 2 3 Y 11 -11.87 1.20 119.70 107.83 D D D C3' O3' P DG DG DC 3 3 4 Y 11 1.85 0.30 108.30 110.15 D D D O4' C1' N1 DC DC DC 4 4 4 N 11 -11.22 1.20 119.70 108.48 D D D C3' O3' P DC DC DC 4 4 5 Y 11 2.09 0.30 108.30 110.39 D D D O4' C1' N1 DC DC DC 5 5 5 N 12 -11.89 1.20 119.70 107.81 D D D C3' O3' P DA DA DC 1 1 2 Y 12 -12.07 1.20 119.70 107.63 D D D C3' O3' P DC DC DG 2 2 3 Y 12 -11.90 1.20 119.70 107.80 D D D C3' O3' P DG DG DC 3 3 4 Y 12 1.88 0.30 108.30 110.18 D D D O4' C1' N1 DC DC DC 4 4 4 N 12 -11.28 1.20 119.70 108.42 D D D C3' O3' P DC DC DC 4 4 5 Y 12 2.00 0.30 108.30 110.30 D D D O4' C1' N1 DC DC DC 5 5 5 N 13 -11.91 1.20 119.70 107.79 D D D C3' O3' P DA DA DC 1 1 2 Y 13 -12.06 1.20 119.70 107.64 D D D C3' O3' P DC DC DG 2 2 3 Y 13 -11.90 1.20 119.70 107.80 D D D C3' O3' P DG DG DC 3 3 4 Y 13 1.87 0.30 108.30 110.17 D D D O4' C1' N1 DC DC DC 4 4 4 N 13 -11.27 1.20 119.70 108.43 D D D C3' O3' P DC DC DC 4 4 5 Y 13 2.03 0.30 108.30 110.33 D D D O4' C1' N1 DC DC DC 5 5 5 N 14 -11.88 1.20 119.70 107.82 D D D C3' O3' P DA DA DC 1 1 2 Y 14 -12.06 1.20 119.70 107.64 D D D C3' O3' P DC DC DG 2 2 3 Y 14 -11.87 1.20 119.70 107.83 D D D C3' O3' P DG DG DC 3 3 4 Y 14 1.87 0.30 108.30 110.17 D D D O4' C1' N1 DC DC DC 4 4 4 N 14 -11.22 1.20 119.70 108.48 D D D C3' O3' P DC DC DC 4 4 5 Y 14 2.03 0.30 108.30 110.33 D D D O4' C1' N1 DC DC DC 5 5 5 N 15 -11.91 1.20 119.70 107.79 D D D C3' O3' P DA DA DC 1 1 2 Y 15 -12.06 1.20 119.70 107.64 D D D C3' O3' P DC DC DG 2 2 3 Y 15 -11.87 1.20 119.70 107.83 D D D C3' O3' P DG DG DC 3 3 4 Y 15 1.88 0.30 108.30 110.18 D D D O4' C1' N1 DC DC DC 4 4 4 N 15 -11.23 1.20 119.70 108.47 D D D C3' O3' P DC DC DC 4 4 5 Y 15 2.06 0.30 108.30 110.36 D D D O4' C1' N1 DC DC DC 5 5 5 N 1 D D P OP3 DA DA 1 1 -0.123 0.012 1.607 1.484 N 2 D D P OP3 DA DA 1 1 -0.123 0.012 1.607 1.484 N 3 D D P OP3 DA DA 1 1 -0.123 0.012 1.607 1.484 N 4 D D P OP3 DA DA 1 1 -0.123 0.012 1.607 1.484 N 5 D D P OP3 DA DA 1 1 -0.123 0.012 1.607 1.484 N 6 D D P OP3 DA DA 1 1 -0.123 0.012 1.607 1.484 N 7 D D P OP3 DA DA 1 1 -0.124 0.012 1.607 1.483 N 8 D D P OP3 DA DA 1 1 -0.123 0.012 1.607 1.484 N 9 D D P OP3 DA DA 1 1 -0.123 0.012 1.607 1.484 N 10 D D P OP3 DA DA 1 1 -0.123 0.012 1.607 1.484 N 11 D D P OP3 DA DA 1 1 -0.123 0.012 1.607 1.484 N 12 D D P OP3 DA DA 1 1 -0.123 0.012 1.607 1.484 N 13 D D P OP3 DA DA 1 1 -0.123 0.012 1.607 1.484 N 14 D D P OP3 DA DA 1 1 -0.123 0.012 1.607 1.484 N 15 D D P OP3 DA DA 1 1 -0.123 0.012 1.607 1.484 N 4 E HIS 11 -172.76 -177.64 5 E ASN 15 -108.61 43.92 8 E HIS 11 -173.51 -177.48 10 E CYS 16 -69.93 -94.47 10 E ARG 17 61.29 74.83 14 E HIS 11 -172.43 -175.68 15 E ARG 17 -142.10 21.11 ZINC-AND SEQUENCE-DEPENDENT BINDING TO NUCLEIC ACIDS BY THE N-TERMINAL ZINC FINGER DOMAIN OF THE HIV-1 NUCLEOCAPSID PROTEIN: NMR STRUCTURE OF THE COMPLEX WITH THE PSI-SITE ANALOG, D/ACGCC 1 N N 2 N N 3 N N E ILE 12 B ILE 12 HELX_P E CYS 16 B CYS 16 5 1 5 metalc 2.310 E CYS 3 B SG CYS 3 1_555 E ZN 19 C ZN ZN 1_555 metalc 2.300 E CYS 6 B SG CYS 6 1_555 E ZN 19 C ZN ZN 1_555 metalc 2.023 E HIS 11 B NE2 HIS 11 1_555 E ZN 19 C ZN ZN 1_555 metalc 2.297 E CYS 16 B SG CYS 16 1_555 E ZN 19 C ZN ZN 1_555 Viral protein/DNA DNA, ZINC FINGER DOMAIN, HIV-1 NUCLEOCAPSID PROTEIN, PSI-SITE ANALOG, Viral protein-DNA COMPLEX GAG_HV1LW UNP 2 389 Q70622 1HVO PDB 1 1HVO 389 406 1HVO 1 18 Q70622 E 1 1 18 1 5 1HVO 1 5 1HVO D 2 1 5 BINDING SITE FOR RESIDUE ZN E 19 E ZN 19 Software 4 E CYS 3 B CYS 3 4 1_555 E CYS 6 B CYS 6 4 1_555 E HIS 11 B HIS 11 4 1_555 E CYS 16 B CYS 16 4 1_555 1 P 1