data_5WKI # _model_server_result.job_id 8r94IRU2E90GZUkXU8jHuQ _model_server_result.datetime_utc '2024-11-24 14:45:46' _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 5wki # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"T","auth_seq_id":307}' # _entry.id 5WKI # _exptl.entry_id 5WKI _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 22.99 _entity.id 9 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'SODIUM 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 94.88 _cell.angle_gamma 90 _cell.entry_id 5WKI _cell.length_a 152.01 _cell.length_b 82.97 _cell.length_c 90.16 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5WKI _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 _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 ? 9 T N N ? 9 X N N # _pdbx_entity_branch.entity_id 5 _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 ? 5 2 1 FUC NAG C1 O1 . O3 HO3 . sing 2 ? 5 3 1 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 5 4 1 FUC NAG C1 O1 . O6 HO6 . 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 5 n E NAG 1 C 1 NAG A 405 NAG 5 n E FUC 2 C 2 FUC A 404 FUC 5 n E NAG 3 C 3 NAG A 406 NAG 5 n E FUC 4 C 4 FUC A 403 FUC # 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 101 A CYS 102 1_555 A SG CYS 165 A CYS 166 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf2 A SG CYS 130 A CYS 131 1_555 A SG CYS 144 A CYS 145 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf3 A SG CYS 205 A CYS 206 1_555 A SG CYS 260 A CYS 261 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf4 B SG CYS 25 B CYS 27 1_555 B SG CYS 80 B CYS 82 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf5 C SG CYS 22 D CYS 22 1_555 C SG CYS 88 D CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf6 C SG CYS 158 D CYS 158 1_555 D SG CYS 176 E CYS 176 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf7 D SG CYS 23 E CYS 23 1_555 D SG CYS 92 E CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf8 D SG CYS 150 E CYS 150 1_555 D SG CYS 215 E CYS 215 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? covale ? covale1 A ND2 ASN 19 A ASN 20 1_555 G C1 NAG . A NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale2 A ND2 ASN 56 A ASN 57 1_555 E C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale3 E O3 NAG . C NAG 1 1_555 E C1 FUC . C FUC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale4 E O4 NAG . C NAG 1 1_555 E C1 NAG . C NAG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale5 E O6 NAG . C NAG 1 1_555 E C1 FUC . C FUC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.414 ? metalc ? metalc1 D O GLY 3 E GLY 3 1_555 X NA NA . E NA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.98 ? # _chem_comp.formula 'Na 1' _chem_comp.formula_weight 22.99 _chem_comp.id NA _chem_comp.mon_nstd_flag . _chem_comp.name 'SODIUM ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 5WKI _atom_sites.fract_transf_matrix[1][1] 0.006579 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000562 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012053 _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] 0.011132 _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 F 6 CUY A 1 401 401 CUY 6UL . G 7 NAG A 1 402 402 NAG NAG . H 8 EDO A 1 407 407 EDO EDO . I 8 EDO A 1 408 408 EDO EDO . J 8 EDO A 1 409 409 EDO EDO . K 8 EDO A 1 410 410 EDO EDO . L 8 EDO A 1 411 411 EDO EDO . M 8 EDO B 1 201 201 EDO EDO . N 8 EDO D 1 301 302 EDO EDO . O 8 EDO D 1 302 303 EDO EDO . P 8 EDO D 1 303 304 EDO EDO . Q 8 EDO D 1 304 305 EDO EDO . R 8 EDO D 1 305 306 EDO EDO . S 8 EDO D 1 306 307 EDO EDO . T 9 NA D 1 307 308 NA NA . U 10 D3D D 1 308 301 D3D PGV . V 11 ACT E 1 301 301 ACT ACT . W 11 ACT E 1 302 302 ACT ACT . X 9 NA E 1 303 303 NA NA . Y 12 CL E 1 304 304 CL CL . Z 13 HOH A 1 501 502 HOH HOH . Z 13 HOH A 2 502 501 HOH HOH . Z 13 HOH A 3 503 503 HOH HOH . Z 13 HOH A 4 504 506 HOH HOH . Z 13 HOH A 5 505 505 HOH HOH . Z 13 HOH A 6 506 504 HOH HOH . Z 13 HOH A 7 507 507 HOH HOH . Z 13 HOH A 8 508 508 HOH HOH . Z 13 HOH A 9 509 509 HOH HOH . Z 13 HOH A 10 510 511 HOH HOH . Z 13 HOH A 11 511 510 HOH HOH . Z 13 HOH A 12 512 513 HOH HOH . Z 13 HOH A 13 513 512 HOH HOH . Z 13 HOH A 14 514 514 HOH HOH . Z 13 HOH A 15 515 517 HOH HOH . Z 13 HOH A 16 516 516 HOH HOH . Z 13 HOH A 17 517 518 HOH HOH . Z 13 HOH A 18 518 519 HOH HOH . Z 13 HOH A 19 519 520 HOH HOH . Z 13 HOH A 20 520 521 HOH HOH . Z 13 HOH A 21 521 522 HOH HOH . Z 13 HOH A 22 522 523 HOH HOH . Z 13 HOH A 23 523 515 HOH HOH . Z 13 HOH A 24 524 524 HOH HOH . Z 13 HOH A 25 525 525 HOH HOH . Z 13 HOH A 26 526 526 HOH HOH . Z 13 HOH A 27 527 527 HOH HOH . Z 13 HOH A 28 528 528 HOH HOH . Z 13 HOH A 29 529 529 HOH HOH . Z 13 HOH A 30 530 530 HOH HOH . Z 13 HOH A 31 531 531 HOH HOH . Z 13 HOH A 32 532 532 HOH HOH . Z 13 HOH A 33 533 533 HOH HOH . Z 13 HOH A 34 534 535 HOH HOH . Z 13 HOH A 35 535 534 HOH HOH . Z 13 HOH A 36 536 536 HOH HOH . Z 13 HOH A 37 537 537 HOH HOH . Z 13 HOH A 38 538 538 HOH HOH . Z 13 HOH A 39 539 539 HOH HOH . Z 13 HOH A 40 540 540 HOH HOH . Z 13 HOH A 41 541 541 HOH HOH . Z 13 HOH A 42 542 542 HOH HOH . Z 13 HOH A 43 543 543 HOH HOH . Z 13 HOH A 44 544 544 HOH HOH . Z 13 HOH A 45 545 545 HOH HOH . AA 13 HOH B 1 301 301 HOH HOH . AA 13 HOH B 2 302 302 HOH HOH . AA 13 HOH B 3 303 303 HOH HOH . AA 13 HOH B 4 304 304 HOH HOH . AA 13 HOH B 5 305 306 HOH HOH . AA 13 HOH B 6 306 305 HOH HOH . AA 13 HOH B 7 307 307 HOH HOH . AA 13 HOH B 8 308 308 HOH HOH . AA 13 HOH B 9 309 309 HOH HOH . AA 13 HOH B 10 310 310 HOH HOH . AA 13 HOH B 11 311 311 HOH HOH . AA 13 HOH B 12 312 312 HOH HOH . AA 13 HOH B 13 313 314 HOH HOH . AA 13 HOH B 14 314 313 HOH HOH . AA 13 HOH B 15 315 315 HOH HOH . AA 13 HOH B 16 316 316 HOH HOH . AA 13 HOH B 17 317 317 HOH HOH . BA 13 HOH D 1 401 401 HOH HOH . BA 13 HOH D 2 402 402 HOH HOH . BA 13 HOH D 3 403 403 HOH HOH . BA 13 HOH D 4 404 404 HOH HOH . BA 13 HOH D 5 405 407 HOH HOH . BA 13 HOH D 6 406 405 HOH HOH . BA 13 HOH D 7 407 406 HOH HOH . BA 13 HOH D 8 408 409 HOH HOH . BA 13 HOH D 9 409 410 HOH HOH . BA 13 HOH D 10 410 408 HOH HOH . BA 13 HOH D 11 411 411 HOH HOH . BA 13 HOH D 12 412 414 HOH HOH . BA 13 HOH D 13 413 412 HOH HOH . BA 13 HOH D 14 414 415 HOH HOH . BA 13 HOH D 15 415 413 HOH HOH . BA 13 HOH D 16 416 416 HOH HOH . BA 13 HOH D 17 417 417 HOH HOH . BA 13 HOH D 18 418 419 HOH HOH . BA 13 HOH D 19 419 418 HOH HOH . BA 13 HOH D 20 420 420 HOH HOH . BA 13 HOH D 21 421 421 HOH HOH . BA 13 HOH D 22 422 422 HOH HOH . BA 13 HOH D 23 423 424 HOH HOH . BA 13 HOH D 24 424 423 HOH HOH . BA 13 HOH D 25 425 425 HOH HOH . BA 13 HOH D 26 426 426 HOH HOH . BA 13 HOH D 27 427 427 HOH HOH . BA 13 HOH D 28 428 428 HOH HOH . BA 13 HOH D 29 429 430 HOH HOH . BA 13 HOH D 30 430 431 HOH HOH . BA 13 HOH D 31 431 429 HOH HOH . BA 13 HOH D 32 432 432 HOH HOH . BA 13 HOH D 33 433 433 HOH HOH . BA 13 HOH D 34 434 434 HOH HOH . BA 13 HOH D 35 435 435 HOH HOH . BA 13 HOH D 36 436 436 HOH HOH . BA 13 HOH D 37 437 437 HOH HOH . BA 13 HOH D 38 438 438 HOH HOH . BA 13 HOH D 39 439 439 HOH HOH . BA 13 HOH D 40 440 440 HOH HOH . BA 13 HOH D 41 441 441 HOH HOH . BA 13 HOH D 42 442 442 HOH HOH . BA 13 HOH D 43 443 443 HOH HOH . BA 13 HOH D 44 444 444 HOH HOH . BA 13 HOH D 45 445 445 HOH HOH . BA 13 HOH D 46 446 446 HOH HOH . BA 13 HOH D 47 447 447 HOH HOH . CA 13 HOH E 1 401 401 HOH HOH . CA 13 HOH E 2 402 405 HOH HOH . CA 13 HOH E 3 403 402 HOH HOH . CA 13 HOH E 4 404 404 HOH HOH . CA 13 HOH E 5 405 406 HOH HOH . CA 13 HOH E 6 406 403 HOH HOH . CA 13 HOH E 7 407 407 HOH HOH . CA 13 HOH E 8 408 408 HOH HOH . CA 13 HOH E 9 409 410 HOH HOH . CA 13 HOH E 10 410 413 HOH HOH . CA 13 HOH E 11 411 411 HOH HOH . CA 13 HOH E 12 412 414 HOH HOH . CA 13 HOH E 13 413 409 HOH HOH . CA 13 HOH E 14 414 412 HOH HOH . CA 13 HOH E 15 415 415 HOH HOH . CA 13 HOH E 16 416 418 HOH HOH . CA 13 HOH E 17 417 419 HOH HOH . CA 13 HOH E 18 418 416 HOH HOH . CA 13 HOH E 19 419 420 HOH HOH . CA 13 HOH E 20 420 417 HOH HOH . CA 13 HOH E 21 421 421 HOH HOH . CA 13 HOH E 22 422 424 HOH HOH . CA 13 HOH E 23 423 423 HOH HOH . CA 13 HOH E 24 424 422 HOH HOH . CA 13 HOH E 25 425 425 HOH HOH . CA 13 HOH E 26 426 426 HOH HOH . CA 13 HOH E 27 427 427 HOH HOH . CA 13 HOH E 28 428 429 HOH HOH . CA 13 HOH E 29 429 428 HOH HOH . CA 13 HOH E 30 430 431 HOH HOH . CA 13 HOH E 31 431 430 HOH HOH . CA 13 HOH E 32 432 432 HOH HOH . CA 13 HOH E 33 433 433 HOH HOH . CA 13 HOH E 34 434 434 HOH HOH . CA 13 HOH E 35 435 435 HOH HOH . CA 13 HOH E 36 436 436 HOH HOH . CA 13 HOH E 37 437 438 HOH HOH . CA 13 HOH E 38 438 437 HOH HOH . CA 13 HOH E 39 439 440 HOH HOH . CA 13 HOH E 40 440 439 HOH HOH . CA 13 HOH E 41 441 441 HOH HOH . CA 13 HOH E 42 442 442 HOH HOH . CA 13 HOH E 43 443 443 HOH HOH . CA 13 HOH E 44 444 444 HOH HOH . CA 13 HOH E 45 445 446 HOH HOH . CA 13 HOH E 46 446 448 HOH HOH . CA 13 HOH E 47 447 447 HOH HOH . CA 13 HOH E 48 448 445 HOH HOH . CA 13 HOH E 49 449 450 HOH HOH . CA 13 HOH E 50 450 449 HOH HOH . CA 13 HOH E 51 451 451 HOH HOH . CA 13 HOH E 52 452 452 HOH HOH . CA 13 HOH E 53 453 453 HOH HOH . CA 13 HOH E 54 454 455 HOH HOH . CA 13 HOH E 55 455 456 HOH HOH . CA 13 HOH E 56 456 454 HOH HOH . CA 13 HOH E 57 457 457 HOH HOH . CA 13 HOH E 58 458 459 HOH HOH . CA 13 HOH E 59 459 458 HOH HOH . CA 13 HOH E 60 460 460 HOH HOH . CA 13 HOH E 61 461 461 HOH HOH . CA 13 HOH E 62 462 463 HOH HOH . CA 13 HOH E 63 463 462 HOH HOH . CA 13 HOH E 64 464 464 HOH HOH . CA 13 HOH E 65 465 465 HOH HOH . CA 13 HOH E 66 466 466 HOH HOH . CA 13 HOH E 67 467 467 HOH HOH . CA 13 HOH E 68 468 469 HOH HOH . CA 13 HOH E 69 469 470 HOH HOH . CA 13 HOH E 70 470 468 HOH HOH . CA 13 HOH E 71 471 471 HOH HOH . CA 13 HOH E 72 472 472 HOH HOH . CA 13 HOH E 73 473 473 HOH HOH . CA 13 HOH E 74 474 474 HOH HOH . CA 13 HOH E 75 475 475 HOH HOH . CA 13 HOH E 76 476 476 HOH HOH . CA 13 HOH E 77 477 477 HOH HOH . CA 13 HOH E 78 478 478 HOH HOH . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol NA _atom_site.label_atom_id NA _atom_site.label_comp_id NA _atom_site.label_seq_id . _atom_site.label_alt_id . _atom_site.pdbx_PDB_ins_code . _atom_site.label_asym_id T _atom_site.label_entity_id 9 _atom_site.Cartn_x 52.433 _atom_site.Cartn_y -0.906 _atom_site.Cartn_z 132.368 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 63.47 _atom_site.pdbx_formal_charge 1 _atom_site.auth_atom_id NA _atom_site.auth_comp_id NA _atom_site.auth_seq_id 307 _atom_site.auth_asym_id D _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 29 _model_server_stats.query_time_ms 436 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 1 #