data_1JVL # _model_server_result.job_id anEusf530IIVHgvfhSVcMw _model_server_result.datetime_utc '2024-11-29 06:30:01' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 1jvl # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":130}' # _entry.id 1JVL # _exptl.entry_id 1JVL _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 58.693 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'NICKEL (II) ION' _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 120 _cell.entry_id 1JVL _cell.length_a 48.605 _cell.length_b 48.605 _cell.length_c 284.809 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1JVL _symmetry.cell_setting hexagonal _symmetry.Int_Tables_number 169 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 61' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 G N N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.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.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _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_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order disulf ? disulf1 A SG CYS 3 A CYS 3 1_555 A SG CYS 26 A CYS 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf2 B SG CYS 3 B CYS 3 1_555 B SG CYS 26 B CYS 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? covale ? covale1 A SG CYS 42 A CYS 42 1_555 I C3 OPP . B OPP 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.821 ? covale ? covale2 B SG CYS 42 B CYS 42 1_555 I C3' OPP . B OPP 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.83 ? metalc ? metalc1 A N ALA 1 A ALA 1 1_555 D NI NI . A NI 130 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.247 ? metalc ? metalc2 A O ALA 1 A ALA 1 1_555 D NI NI . A NI 130 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.145 ? metalc ? metalc3 A ND1 HIS 46 A HIS 46 1_555 C CU CU . A CU 129 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? metalc ? metalc4 A NE2 HIS 83 A HIS 83 5_564 G NI NI . B NI 130 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.181 ? metalc ? metalc5 A SG CYS 112 A CYS 112 1_555 C CU CU . A CU 129 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.177 ? metalc ? metalc6 A ND1 HIS 117 A HIS 117 1_555 C CU CU . A CU 129 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.161 ? metalc ? metalc7 D NI NI . A NI 130 1_555 E O2 144 . A 144 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.086 ? metalc ? metalc8 D NI NI . A NI 130 1_555 J O HOH . A HOH 553 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? metalc ? metalc9 D NI NI . A NI 130 1_555 B NE2 HIS 83 B HIS 83 6_545 ? ? ? ? ? ? ? ? ? ? ? ? 2.199 ? metalc ? metalc10 B N ALA 1 B ALA 1 1_555 G NI NI . B NI 130 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.247 ? metalc ? metalc11 B O ALA 1 B ALA 1 1_555 G NI NI . B NI 130 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.152 ? metalc ? metalc12 B ND1 HIS 46 B HIS 46 1_555 F CU CU . B CU 129 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? metalc ? metalc13 B SG CYS 112 B CYS 112 1_555 F CU CU . B CU 129 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.19 ? metalc ? metalc14 B ND1 HIS 117 B HIS 117 1_555 F CU CU . B CU 129 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.163 ? metalc ? metalc15 G NI NI . B NI 130 1_555 H O2 144 . B 144 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? metalc ? metalc16 G NI NI . B NI 130 1_555 K O HOH . B HOH 557 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? # _chem_comp.formula 'Ni 2' _chem_comp.formula_weight 58.693 _chem_comp.id NI _chem_comp.mon_nstd_flag . _chem_comp.name 'NICKEL (II) ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 1JVL _atom_sites.fract_transf_matrix[1][1] 0.020574 _atom_sites.fract_transf_matrix[1][2] 0.011878 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.023757 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.003511 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code C 2 CU A 1 129 129 CU CU . D 3 NI A 1 130 130 NI NI . E 4 144 A 1 503 503 144 144 . F 2 CU B 1 129 129 CU CU . G 3 NI B 1 130 130 NI NI . H 4 144 B 1 504 504 144 144 . I 5 OPP B 1 505 505 OPP OPP . J 6 HOH A 1 504 1 HOH HOH . J 6 HOH A 2 505 2 HOH HOH . J 6 HOH A 3 506 3 HOH HOH . J 6 HOH A 4 507 4 HOH HOH . J 6 HOH A 5 508 5 HOH HOH . J 6 HOH A 6 509 6 HOH HOH . J 6 HOH A 7 510 7 HOH HOH . J 6 HOH A 8 511 8 HOH HOH . J 6 HOH A 9 512 9 HOH HOH . J 6 HOH A 10 513 10 HOH HOH . J 6 HOH A 11 514 11 HOH HOH . J 6 HOH A 12 515 12 HOH HOH . J 6 HOH A 13 516 13 HOH HOH . J 6 HOH A 14 517 14 HOH HOH . J 6 HOH A 15 518 15 HOH HOH . J 6 HOH A 16 519 16 HOH HOH . J 6 HOH A 17 520 17 HOH HOH . J 6 HOH A 18 521 18 HOH HOH . J 6 HOH A 19 522 19 HOH HOH . J 6 HOH A 20 523 20 HOH HOH . J 6 HOH A 21 524 21 HOH HOH . J 6 HOH A 22 525 22 HOH HOH . J 6 HOH A 23 526 23 HOH HOH . J 6 HOH A 24 527 24 HOH HOH . J 6 HOH A 25 528 25 HOH HOH . J 6 HOH A 26 529 26 HOH HOH . J 6 HOH A 27 530 27 HOH HOH . J 6 HOH A 28 531 28 HOH HOH . J 6 HOH A 29 532 29 HOH HOH . J 6 HOH A 30 533 30 HOH HOH . J 6 HOH A 31 534 31 HOH HOH . J 6 HOH A 32 535 32 HOH HOH . J 6 HOH A 33 536 33 HOH HOH . J 6 HOH A 34 537 34 HOH HOH . J 6 HOH A 35 538 35 HOH HOH . J 6 HOH A 36 539 36 HOH HOH . J 6 HOH A 37 540 37 HOH HOH . J 6 HOH A 38 541 38 HOH HOH . J 6 HOH A 39 542 39 HOH HOH . J 6 HOH A 40 543 40 HOH HOH . J 6 HOH A 41 544 41 HOH HOH . J 6 HOH A 42 545 42 HOH HOH . J 6 HOH A 43 546 43 HOH HOH . J 6 HOH A 44 547 44 HOH HOH . J 6 HOH A 45 548 45 HOH HOH . J 6 HOH A 46 549 46 HOH HOH . J 6 HOH A 47 550 47 HOH HOH . J 6 HOH A 48 551 48 HOH HOH . J 6 HOH A 49 552 49 HOH HOH . J 6 HOH A 50 553 51 HOH HOH . J 6 HOH A 51 554 52 HOH HOH . J 6 HOH A 52 555 53 HOH HOH . J 6 HOH A 53 556 54 HOH HOH . J 6 HOH A 54 557 111 HOH HOH . J 6 HOH A 55 558 112 HOH HOH . J 6 HOH A 56 559 113 HOH HOH . K 6 HOH B 1 506 50 HOH HOH . K 6 HOH B 2 507 55 HOH HOH . K 6 HOH B 3 508 56 HOH HOH . K 6 HOH B 4 509 57 HOH HOH . K 6 HOH B 5 510 58 HOH HOH . K 6 HOH B 6 511 59 HOH HOH . K 6 HOH B 7 512 60 HOH HOH . K 6 HOH B 8 513 61 HOH HOH . K 6 HOH B 9 514 62 HOH HOH . K 6 HOH B 10 515 63 HOH HOH . K 6 HOH B 11 516 64 HOH HOH . K 6 HOH B 12 517 65 HOH HOH . K 6 HOH B 13 518 66 HOH HOH . K 6 HOH B 14 519 67 HOH HOH . K 6 HOH B 15 520 68 HOH HOH . K 6 HOH B 16 521 69 HOH HOH . K 6 HOH B 17 522 70 HOH HOH . K 6 HOH B 18 523 71 HOH HOH . K 6 HOH B 19 524 72 HOH HOH . K 6 HOH B 20 525 73 HOH HOH . K 6 HOH B 21 526 74 HOH HOH . K 6 HOH B 22 527 75 HOH HOH . K 6 HOH B 23 528 76 HOH HOH . K 6 HOH B 24 529 77 HOH HOH . K 6 HOH B 25 530 78 HOH HOH . K 6 HOH B 26 531 79 HOH HOH . K 6 HOH B 27 532 80 HOH HOH . K 6 HOH B 28 533 81 HOH HOH . K 6 HOH B 29 534 82 HOH HOH . K 6 HOH B 30 535 83 HOH HOH . K 6 HOH B 31 536 84 HOH HOH . K 6 HOH B 32 537 85 HOH HOH . K 6 HOH B 33 538 86 HOH HOH . K 6 HOH B 34 539 87 HOH HOH . K 6 HOH B 35 540 88 HOH HOH . K 6 HOH B 36 541 89 HOH HOH . K 6 HOH B 37 542 90 HOH HOH . K 6 HOH B 38 543 91 HOH HOH . K 6 HOH B 39 544 92 HOH HOH . K 6 HOH B 40 545 93 HOH HOH . K 6 HOH B 41 546 94 HOH HOH . K 6 HOH B 42 547 95 HOH HOH . K 6 HOH B 43 548 96 HOH HOH . K 6 HOH B 44 549 97 HOH HOH . K 6 HOH B 45 550 98 HOH HOH . K 6 HOH B 46 551 99 HOH HOH . K 6 HOH B 47 552 100 HOH HOH . K 6 HOH B 48 553 101 HOH HOH . K 6 HOH B 49 554 102 HOH HOH . K 6 HOH B 50 555 103 HOH HOH . K 6 HOH B 51 556 104 HOH HOH . K 6 HOH B 52 557 105 HOH HOH . K 6 HOH B 53 558 106 HOH HOH . K 6 HOH B 54 559 107 HOH HOH . K 6 HOH B 55 560 108 HOH HOH . K 6 HOH B 56 561 109 HOH HOH . K 6 HOH B 57 562 110 HOH HOH . K 6 HOH B 58 563 114 HOH HOH . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol NI _atom_site.label_atom_id NI _atom_site.label_comp_id NI _atom_site.label_seq_id . _atom_site.label_alt_id . _atom_site.pdbx_PDB_ins_code . _atom_site.label_asym_id D _atom_site.label_entity_id 3 _atom_site.Cartn_x 19.775 _atom_site.Cartn_y -15.193 _atom_site.Cartn_z 49.314 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 40.12 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NI _atom_site.auth_comp_id NI _atom_site.auth_seq_id 130 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 499 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 1 #