1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Capili, A.D. Schultz, D.C. Rauscher III, F.J. Borden, K.L.B. 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 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 H13 N O2 131.173 y ISOLEUCINE L-peptide linking C6 H13 N O2 131.173 y LEUCINE 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 C3 H7 N O3 105.093 y SERINE 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 EMBO J. EMJODG 0897 0261-4189 20 165 177 10.1093/emboj/20.1.165 11226167 Solution structure of the PHD domain from the KAP-1 corepressor: structural determinants for PHD, RING and LIM zinc-binding domains. 2001 10.2210/pdb1fp0/pdb pdb_00001fp0 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 9939.204 KAP-1 COREPRESSOR PHD DOMAIN 1 man polymer 65.409 ZINC ION 2 syn non-polymer TRANSCRIPTION INTERMEDIARY FACTOR 1-BETA, NUCLEAR COREPRESSOR, KAP-1, KRAB-ASSOCIATED PROTEIN 1 no no MRGSHHHHHHGSDIIDEFGTLDDSATICRVCQKPGDLVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVLPDLKEEDV DLQACKLN MRGSHHHHHHGSDIIDEFGTLDDSATICRVCQKPGDLVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVLPDLKEEDV DLQACKLN 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 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 human Homo Escherichia sample 9606 Homo sapiens 562 Escherichia coli PLASMID PQE50 database_2 pdbx_struct_assembly pdbx_struct_conn_angle pdbx_struct_oper_list struct_conn struct_ref_seq_dif struct_site repository Initial release Version format compliance Version format compliance Database references Derived calculations 1 0 2001-01-24 1 1 2008-04-27 1 2 2011-07-13 1 3 2022-02-23 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.value _struct_conn.pdbx_dist_value _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_ref_seq_dif.details _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id RCSB Y RCSB 2000-08-29 REL ZN ZINC ION First 17 residues (MRGSHHHHHHGSDIIDE) and last 9 residues (VDLQACKLN) do not belong to the natural protein molecule, residues 618 to 679 corresponds to KAP-1, structured region corresponds to residues 627-670 which contain the PHD domain 1 7.50 AMBIENT 303 K distance geometry and simulated annealing 1 closest to the average 1.5-3.0 mM 15N-labelled or unlabelled KAP-1 PHD, 20 mM NaH2PO4, 500 mM NaCl, 5 mM DTT, pH 7.5 90% H2O/10% D2O 1.5-3.0 mM unlabelled KAP-1 PHD, 20 mM NaH2PO4, 500 mM NaCl, 5 mM DTT, pH 7.5 100% D2O Brunger refinement X-PLOR 3.851 500 Bruker DRX ZN 89 2 ZN ZN 89 A ZN 90 2 ZN ZN 90 A MET 1 n 1 MET 1 A ARG 2 n 2 ARG 2 A GLY 3 n 3 GLY 3 A SER 4 n 4 SER 4 A HIS 5 n 5 HIS 5 A HIS 6 n 6 HIS 6 A HIS 7 n 7 HIS 7 A HIS 8 n 8 HIS 8 A HIS 9 n 9 HIS 9 A HIS 10 n 10 HIS 10 A GLY 11 n 11 GLY 11 A SER 12 n 12 SER 12 A ASP 13 n 13 ASP 13 A ILE 14 n 14 ILE 14 A ILE 15 n 15 ILE 15 A ASP 16 n 16 ASP 16 A GLU 17 n 17 GLU 17 A PHE 18 n 18 PHE 18 A GLY 19 n 19 GLY 19 A THR 20 n 20 THR 20 A LEU 21 n 21 LEU 21 A ASP 22 n 22 ASP 22 A ASP 23 n 23 ASP 23 A SER 24 n 24 SER 24 A ALA 25 n 25 ALA 25 A THR 26 n 26 THR 26 A ILE 27 n 27 ILE 27 A CYS 28 n 28 CYS 28 A ARG 29 n 29 ARG 29 A VAL 30 n 30 VAL 30 A CYS 31 n 31 CYS 31 A GLN 32 n 32 GLN 32 A LYS 33 n 33 LYS 33 A PRO 34 n 34 PRO 34 A GLY 35 n 35 GLY 35 A ASP 36 n 36 ASP 36 A LEU 37 n 37 LEU 37 A VAL 38 n 38 VAL 38 A MET 39 n 39 MET 39 A CYS 40 n 40 CYS 40 A ASN 41 n 41 ASN 41 A GLN 42 n 42 GLN 42 A CYS 43 n 43 CYS 43 A GLU 44 n 44 GLU 44 A PHE 45 n 45 PHE 45 A CYS 46 n 46 CYS 46 A PHE 47 n 47 PHE 47 A HIS 48 n 48 HIS 48 A LEU 49 n 49 LEU 49 A ASP 50 n 50 ASP 50 A CYS 51 n 51 CYS 51 A HIS 52 n 52 HIS 52 A LEU 53 n 53 LEU 53 A PRO 54 n 54 PRO 54 A ALA 55 n 55 ALA 55 A LEU 56 n 56 LEU 56 A GLN 57 n 57 GLN 57 A ASP 58 n 58 ASP 58 A VAL 59 n 59 VAL 59 A PRO 60 n 60 PRO 60 A GLY 61 n 61 GLY 61 A GLU 62 n 62 GLU 62 A GLU 63 n 63 GLU 63 A TRP 64 n 64 TRP 64 A SER 65 n 65 SER 65 A CYS 66 n 66 CYS 66 A SER 67 n 67 SER 67 A LEU 68 n 68 LEU 68 A CYS 69 n 69 CYS 69 A HIS 70 n 70 HIS 70 A VAL 71 n 71 VAL 71 A LEU 72 n 72 LEU 72 A PRO 73 n 73 PRO 73 A ASP 74 n 74 ASP 74 A LEU 75 n 75 LEU 75 A LYS 76 n 76 LYS 76 A GLU 77 n 77 GLU 77 A GLU 78 n 78 GLU 78 A ASP 79 n 79 ASP 79 A VAL 80 n 80 VAL 80 A ASP 81 n 81 ASP 81 A LEU 82 n 82 LEU 82 A GLN 83 n 83 GLN 83 A ALA 84 n 84 ALA 84 A CYS 85 n 85 CYS 85 A LYS 86 n 86 LYS 86 A LEU 87 n 87 LEU 87 A ASN 88 n 88 ASN 88 A author_defined_assembly 1 monomeric A CYS 28 A SG CYS 28 1_555 A ZN 90 C ZN ZN 1_555 A CYS 31 A SG CYS 31 1_555 112.0 A CYS 28 A SG CYS 28 1_555 A ZN 90 C ZN ZN 1_555 A HIS 48 A ND1 HIS 48 1_555 109.9 A CYS 31 A SG CYS 31 1_555 A ZN 90 C ZN ZN 1_555 A HIS 48 A ND1 HIS 48 1_555 108.3 A CYS 28 A SG CYS 28 1_555 A ZN 90 C ZN ZN 1_555 A CYS 51 A SG CYS 51 1_555 110.9 A CYS 31 A SG CYS 31 1_555 A ZN 90 C ZN ZN 1_555 A CYS 51 A SG CYS 51 1_555 108.6 A HIS 48 A ND1 HIS 48 1_555 A ZN 90 C ZN ZN 1_555 A CYS 51 A SG CYS 51 1_555 107.0 A CYS 40 A SG CYS 40 1_555 A ZN 89 B ZN ZN 1_555 A CYS 43 A SG CYS 43 1_555 106.4 A CYS 40 A SG CYS 40 1_555 A ZN 89 B ZN ZN 1_555 A CYS 66 A SG CYS 66 1_555 111.0 A CYS 43 A SG CYS 43 1_555 A ZN 89 B ZN ZN 1_555 A CYS 66 A SG CYS 66 1_555 110.2 A CYS 40 A SG CYS 40 1_555 A ZN 89 B ZN ZN 1_555 A CYS 69 A SG CYS 69 1_555 109.5 A CYS 43 A SG CYS 43 1_555 A ZN 89 B ZN ZN 1_555 A CYS 69 A SG CYS 69 1_555 109.1 A CYS 66 A SG CYS 66 1_555 A ZN 89 B ZN ZN 1_555 A CYS 69 A SG CYS 69 1_555 110.6 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 A O VAL 38 A O VAL 38 A N PHE 47 A N PHE 47 1 A A O H LEU ALA 53 55 1.53 1 A ARG 2 0.279 SIDE CHAIN 1 A ARG 29 0.317 SIDE CHAIN 1 A SER 4 -163.05 30.42 1 A HIS 8 55.89 175.68 1 A HIS 9 -146.37 -143.53 1 A HIS 10 -41.93 -82.44 1 A ASP 13 178.08 -50.47 1 A ILE 14 80.02 -24.91 1 A ILE 15 57.47 121.06 1 A THR 20 38.56 34.63 1 A LEU 21 -139.57 -71.38 1 A ASP 22 -81.86 -150.67 1 A ASP 23 55.51 19.81 1 A SER 24 178.03 178.38 1 A ALA 25 70.64 -135.38 1 A THR 26 -39.89 170.30 1 A CYS 31 -160.21 -41.12 1 A LYS 33 -140.88 -66.55 1 A ASP 36 44.28 104.18 1 A LEU 37 -168.35 105.86 1 A ASN 41 -69.34 5.58 1 A CYS 43 -153.92 -84.51 1 A GLU 44 -175.95 33.37 1 A PHE 47 -139.06 -157.40 1 A LEU 49 -69.49 9.08 1 A HIS 52 -88.79 -87.31 1 A PRO 54 -63.22 63.90 1 A ALA 55 177.18 42.52 1 A GLU 62 58.73 -108.90 1 A GLU 63 -99.66 -151.36 1 A TRP 64 -74.91 -102.24 1 A SER 65 172.62 37.42 1 A CYS 66 57.50 163.62 1 A SER 67 -135.06 -141.70 1 A VAL 71 -111.23 52.71 1 A CYS 85 -59.14 -144.70 SOLUTION STRUCTURE OF THE PHD DOMAIN FROM THE KAP-1 COREPRESSOR 1 N N 2 N N 2 N N metalc 2.344 A CYS 28 A SG CYS 28 1_555 A ZN 90 C ZN ZN 1_555 metalc 2.312 A CYS 31 A SG CYS 31 1_555 A ZN 90 C ZN ZN 1_555 metalc 2.276 A CYS 40 A SG CYS 40 1_555 A ZN 89 B ZN ZN 1_555 metalc 2.297 A CYS 43 A SG CYS 43 1_555 A ZN 89 B ZN ZN 1_555 metalc 1.977 A HIS 48 A ND1 HIS 48 1_555 A ZN 90 C ZN ZN 1_555 metalc 2.293 A CYS 51 A SG CYS 51 1_555 A ZN 90 C ZN ZN 1_555 metalc 2.317 A CYS 66 A SG CYS 66 1_555 A ZN 89 B ZN ZN 1_555 metalc 2.299 A CYS 69 A SG CYS 69 1_555 A ZN 89 B ZN ZN 1_555 TRANSCRIPTION PHD domain, C3HC4 type zinc binding domain, NMR-structure, TRANSCRIPTION TIF1B_HUMAN UNP 1 619 Q13263 GTLDDSATICRVCQKPGDLVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVLPDLKEED 619 679 1FP0 19 79 Q13263 A 1 19 79 1 expression tag MET 1 1FP0 A Q13263 UNP 1 1 expression tag ARG 2 1FP0 A Q13263 UNP 2 1 expression tag GLY 3 1FP0 A Q13263 UNP 3 1 expression tag SER 4 1FP0 A Q13263 UNP 4 1 expression tag HIS 5 1FP0 A Q13263 UNP 5 1 expression tag HIS 6 1FP0 A Q13263 UNP 6 1 expression tag HIS 7 1FP0 A Q13263 UNP 7 1 expression tag HIS 8 1FP0 A Q13263 UNP 8 1 expression tag HIS 9 1FP0 A Q13263 UNP 9 1 expression tag HIS 10 1FP0 A Q13263 UNP 10 1 expression tag GLY 11 1FP0 A Q13263 UNP 11 1 expression tag SER 12 1FP0 A Q13263 UNP 12 1 expression tag ASP 13 1FP0 A Q13263 UNP 13 1 expression tag ILE 14 1FP0 A Q13263 UNP 14 1 expression tag ILE 15 1FP0 A Q13263 UNP 15 1 expression tag ASP 16 1FP0 A Q13263 UNP 16 1 expression tag GLU 17 1FP0 A Q13263 UNP 17 1 expression tag PHE 18 1FP0 A Q13263 UNP 18 1 cloning artifact VAL 80 1FP0 A Q13263 UNP 80 1 cloning artifact ASP 81 1FP0 A Q13263 UNP 81 1 cloning artifact LEU 82 1FP0 A Q13263 UNP 82 1 cloning artifact GLN 83 1FP0 A Q13263 UNP 83 1 cloning artifact ALA 84 1FP0 A Q13263 UNP 84 1 cloning artifact CYS 85 1FP0 A Q13263 UNP 85 1 cloning artifact LYS 86 1FP0 A Q13263 UNP 86 1 cloning artifact LEU 87 1FP0 A Q13263 UNP 87 1 cloning artifact ASN 88 1FP0 A Q13263 UNP 88 3 anti-parallel A VAL 38 A VAL 38 A CYS 40 A CYS 40 A PHE 45 A PHE 45 A PHE 47 A PHE 47 A TRP 64 A TRP 64 A SER 67 A SER 67 BINDING SITE FOR RESIDUE ZN A 89 A ZN 89 Software 5 BINDING SITE FOR RESIDUE ZN A 90 A ZN 90 Software 6 A CYS 40 A CYS 40 5 1_555 A GLN 42 A GLN 42 5 1_555 A CYS 43 A CYS 43 5 1_555 A CYS 66 A CYS 66 5 1_555 A CYS 69 A CYS 69 5 1_555 A CYS 28 A CYS 28 6 1_555 A VAL 30 A VAL 30 6 1_555 A CYS 31 A CYS 31 6 1_555 A PHE 47 A PHE 47 6 1_555 A HIS 48 A HIS 48 6 1_555 A CYS 51 A CYS 51 6 1_555 1 P 1