data_5XWD # _model_server_result.job_id JobpuY-R5tUez4kdKqmffA _model_server_result.datetime_utc '2024-11-24 02:16:53' _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 5xwd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":717}' # _entry.id 5XWD # _exptl.entry_id 5XWD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 65.409 _entity.id 6 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 'ZINC ION' _entity.pdbx_number_of_molecules 20 _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 5XWD _cell.length_a 203.428 _cell.length_b 203.428 _cell.length_c 113.817 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5XWD _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65 2 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_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,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA _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 ? 6 L N N ? 6 M N N ? 6 N N N ? 6 O N N ? 6 P N N ? 6 Q N N ? 6 R N N ? 6 S N N ? 6 T N N ? 6 U N N ? 6 V N N ? 6 W N N ? 6 X N N ? 6 Y N N ? 6 Z N N ? 6 AA N N ? 6 BA N N ? 6 CA N N ? 6 DA N N ? 6 EA N N # _pdbx_entity_branch.entity_id 4 _pdbx_entity_branch.type oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 4 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 4 4 3 MAN BMA C1 O1 . O3 HO3 . sing 4 ? 4 5 4 NAG MAN C1 O1 . O2 HO2 . sing 5 ? 4 6 3 MAN BMA C1 O1 . O6 HO6 . sing 6 ? 4 7 6 NAG MAN C1 O1 . O2 HO2 . sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 4 n D NAG 1 B 1 NAG A 1328 NAG 4 n D NAG 2 B 2 NAG A 1329 NAG 4 n D BMA 3 B 3 BMA A 1330 BMA 4 n D MAN 4 B 4 MAN A 1331 MAN 4 n D NAG 5 B 5 NAG A 1332 NAG 4 n D MAN 6 B 6 MAN A 1334 MAN 4 n D NAG 7 B 7 NAG A 1335 NAG # 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 31 A CYS 7 1_555 A SG CYS 58 A CYS 34 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf2 A SG CYS 157 A CYS 133 1_555 A SG CYS 187 A CYS 163 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? disulf ? disulf3 A SG CYS 190 A CYS 166 1_555 A SG CYS 199 A CYS 175 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? disulf ? disulf4 A SG CYS 194 A CYS 170 1_555 A SG CYS 207 A CYS 183 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? disulf ? disulf5 A SG CYS 215 A CYS 191 1_555 A SG CYS 223 A CYS 199 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf6 A SG CYS 219 A CYS 195 1_555 A SG CYS 231 A CYS 207 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? disulf ? disulf7 A SG CYS 232 A CYS 208 1_555 A SG CYS 240 A CYS 216 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? disulf ? disulf8 A SG CYS 236 A CYS 212 1_555 A SG CYS 248 A CYS 224 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf9 A SG CYS 251 A CYS 227 1_555 A SG CYS 260 A CYS 236 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? disulf ? disulf10 A SG CYS 264 A CYS 240 1_555 A SG CYS 291 A CYS 267 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? disulf ? disulf11 A SG CYS 295 A CYS 271 1_555 A SG CYS 307 A CYS 283 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf12 A SG CYS 311 A CYS 287 1_555 A SG CYS 326 A CYS 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf13 A SG CYS 329 A CYS 305 1_555 A SG CYS 333 A CYS 309 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? disulf ? disulf14 A SG CYS 337 A CYS 313 1_555 A SG CYS 362 A CYS 338 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf15 A SG CYS 470 A CYS 446 1_555 A SG CYS 499 A CYS 475 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf16 A SG CYS 506 A CYS 482 1_555 A SG CYS 515 A CYS 491 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf17 A SG CYS 510 A CYS 486 1_555 A SG CYS 523 A CYS 499 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? disulf ? disulf18 A SG CYS 526 A CYS 502 1_555 A SG CYS 535 A CYS 511 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf19 A SG CYS 539 A CYS 515 1_555 A SG CYS 555 A CYS 531 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf20 A SG CYS 558 A CYS 534 1_555 A SG CYS 571 A CYS 547 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf21 A SG CYS 562 A CYS 538 1_555 A SG CYS 579 A CYS 555 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf22 A SG CYS 582 A CYS 558 1_555 A SG CYS 591 A CYS 567 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf23 A SG CYS 595 A CYS 571 1_555 A SG CYS 617 A CYS 593 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf24 A SG CYS 620 A CYS 596 1_555 A SG CYS 628 A CYS 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf25 A SG CYS 624 A CYS 600 1_555 A SG CYS 636 A CYS 612 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf26 B SG CYS 29 H CYS 22 1_555 B SG CYS 104 H CYS 97 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf27 C SG CYS 29 D CYS 23 1_555 C SG CYS 94 D CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? covale ? covale1 A ND2 ASN 56 A ASN 32 1_555 E C1 NAG . A NAG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? covale ? covale2 A ND2 ASN 175 A ASN 151 1_555 F C1 NAG . A NAG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale3 A ND2 ASN 196 A ASN 172 1_555 G C1 NAG . A NAG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale4 A ND2 ASN 352 A ASN 328 1_555 D C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.466 ? covale ? covale5 A ND2 ASN 361 A ASN 337 1_555 H C1 NAG . A NAG 711 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale6 A ND2 ASN 444 A ASN 420 1_555 I C1 NAG . A NAG 712 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale7 A ND2 ASN 528 A ASN 504 1_555 J C1 NAG . A NAG 713 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale8 A ND2 ASN 568 A ASN 544 1_555 K C1 NAG . A NAG 714 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? covale ? covale9 D O4 NAG . B NAG 1 1_555 D C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale10 D O4 NAG . B NAG 2 1_555 D C1 BMA . B BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale11 D O3 BMA . B BMA 3 1_555 D C1 MAN . B MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale12 D O6 BMA . B BMA 3 1_555 D C1 MAN . B MAN 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale13 D O2 MAN . B MAN 4 1_555 D C1 NAG . B NAG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.467 ? covale ? covale14 D O2 MAN . B MAN 6 1_555 D C1 NAG . B NAG 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? metalc ? metalc1 A OE2 GLU 45 A GLU 21 1_555 L ZN ZN . A ZN 715 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.271 ? metalc ? metalc2 A ND1 HIS 145 A HIS 121 1_555 M ZN ZN . A ZN 716 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.694 ? metalc ? metalc3 A OE1 GLN 276 A GLN 252 1_555 N ZN ZN . A ZN 717 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? metalc ? metalc4 A OD2 ASP 303 A ASP 279 1_555 O ZN ZN . A ZN 718 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.15 ? metalc ? metalc5 A OD1 ASP 303 A ASP 279 1_555 X ZN ZN . A ZN 727 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.64 ? metalc ? metalc6 A ND1 HIS 304 A HIS 280 1_555 Z ZN ZN . A ZN 729 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.478 ? metalc ? metalc7 A OE1 GLU 344 A GLU 320 1_555 V ZN ZN . A ZN 725 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.28 ? metalc ? metalc8 A NE2 HIS 358 A HIS 334 1_555 P ZN ZN . A ZN 719 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.311 ? metalc ? metalc9 A NE2 HIS 358 A HIS 334 1_555 V ZN ZN . A ZN 725 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.485 ? metalc ? metalc10 A OD1 ASP 393 A ASP 369 1_555 Q ZN ZN . A ZN 720 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? metalc ? metalc11 A NH1 ARG 414 A ARG 390 1_555 Q ZN ZN . A ZN 720 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.086 ? metalc ? metalc12 A OD2 ASP 416 A ASP 392 1_555 S ZN ZN . A ZN 722 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.332 ? metalc ? metalc13 A ND1 HIS 418 A HIS 394 1_555 Q ZN ZN . A ZN 720 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.583 ? metalc ? metalc14 A OD2 ASP 577 A ASP 553 1_555 Y ZN ZN . A ZN 728 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.245 ? metalc ? metalc15 A NE2 HIS 584 A HIS 560 1_555 R ZN ZN . A ZN 721 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.183 ? metalc ? metalc16 A NE2 HIS 590 A HIS 566 1_555 N ZN ZN . A ZN 717 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.108 ? metalc ? metalc17 A NE2 HIS 615 A HIS 591 1_555 R ZN ZN . A ZN 721 11_654 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? metalc ? metalc18 A ND1 HIS 618 A HIS 594 1_555 U ZN ZN . A ZN 724 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.228 ? metalc ? metalc19 B OG SER 83 H SER 76 1_555 AA ZN ZN . H ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? metalc ? metalc20 B NH1 ARG 106 H ARG 99 1_555 BA ZN ZN . H ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.112 ? metalc ? metalc21 B OD2 ASP 115 H ASP 108 1_555 BA ZN ZN . H ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.001 ? metalc ? metalc22 B OD1 ASP 115 H ASP 108 1_555 CA ZN ZN . H ZN 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.573 ? metalc ? metalc23 B OD2 ASP 115 H ASP 108 1_555 CA ZN ZN . H ZN 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? metalc ? metalc24 AA ZN ZN . H ZN 201 1_555 D O3 NAG . B NAG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.472 ? metalc ? metalc25 C OG SER 8 D SER 2 1_555 DA ZN ZN . D ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.174 ? metalc ? metalc26 C ND1 HIS 103 D HIS 97 1_555 DA ZN ZN . D ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.47 ? metalc ? metalc27 C NE2 HIS 103 D HIS 97 1_555 EA ZN ZN . D ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.353 ? # _chem_comp.formula 'Zn 2' _chem_comp.formula_weight 65.409 _chem_comp.id ZN _chem_comp.mon_nstd_flag . _chem_comp.name 'ZINC ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 5XWD _atom_sites.fract_transf_matrix[1][1] 0.004916 _atom_sites.fract_transf_matrix[1][2] 0.002838 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.005676 _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] 0.008786 _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 E 5 NAG A 1 701 1032 NAG NAG . F 5 NAG A 1 702 1151 NAG NAG . G 5 NAG A 1 703 1172 NAG NAG . H 5 NAG A 1 711 1337 NAG NAG . I 5 NAG A 1 712 1420 NAG NAG . J 5 NAG A 1 713 1504 NAG NAG . K 5 NAG A 1 714 1544 NAG NAG . L 6 ZN A 1 715 1 ZN ZN . M 6 ZN A 1 716 2 ZN ZN . N 6 ZN A 1 717 3 ZN ZN . O 6 ZN A 1 718 4 ZN ZN . P 6 ZN A 1 719 5 ZN ZN . Q 6 ZN A 1 720 6 ZN ZN . R 6 ZN A 1 721 7 ZN ZN . S 6 ZN A 1 722 10 ZN ZN . T 6 ZN A 1 723 11 ZN ZN . U 6 ZN A 1 724 12 ZN ZN . V 6 ZN A 1 725 14 ZN ZN . W 6 ZN A 1 726 15 ZN ZN . X 6 ZN A 1 727 16 ZN ZN . Y 6 ZN A 1 728 19 ZN ZN . Z 6 ZN A 1 729 20 ZN ZN . AA 6 ZN H 1 201 13 ZN ZN . BA 6 ZN H 1 202 17 ZN ZN . CA 6 ZN H 1 203 21 ZN ZN . DA 6 ZN D 1 201 8 ZN ZN . EA 6 ZN D 1 202 9 ZN ZN . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol ZN _atom_site.label_atom_id ZN _atom_site.label_comp_id ZN _atom_site.label_seq_id . _atom_site.label_alt_id . _atom_site.pdbx_PDB_ins_code . _atom_site.label_asym_id N _atom_site.label_entity_id 6 _atom_site.Cartn_x 96.585 _atom_site.Cartn_y -36.555 _atom_site.Cartn_z -9.339 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 177.26 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id ZN _atom_site.auth_comp_id ZN _atom_site.auth_seq_id 717 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 312 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 1 #