data_2JXR # _model_server_result.job_id fOf8QglGAthNbxK2xfu65g _model_server_result.datetime_utc '2024-11-28 22:57:10' _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 2jxr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":337}' # _entry.id 2JXR # _exptl.entry_id 2JXR _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 4 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 1 _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 2JXR _cell.length_a 86.7 _cell.length_b 86.7 _cell.length_c 110.4 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2JXR _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 32 2 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA dimeric 2 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E 1 1 A,B,C,D,E 2 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 6_555 -x,-x+y,-z+2/3 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 0 0 73.6 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 2 _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 ? 2 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 2 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 2 4 3 BMA BMA C1 O1 . O3 HO3 . sing 4 ? 2 5 4 MAN BMA 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 2 n B NAG 1 B 1 NAG ? 332 NAG 2 n B NAG 2 B 2 NAG ? 333 NAG 2 n B BMA 3 B 3 BMA ? 334 MAN 2 n B BMA 4 B 4 BMA ? 335 MAN 2 n B MAN 5 B 5 MAN ? 336 MAN # 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 46 A CYS 45 1_555 A SG CYS 51 A CYS 50 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.955 ? disulf ? disulf2 A SG CYS 252 A CYS 249 1_555 A SG CYS 285 A CYS 282 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.955 ? covale ? covale1 A ND2 ASN 68 A ASN 67 1_555 B C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.398 ? covale ? covale2 A ND2 ASN 269 A ASN 266 1_555 D C1 NAG . A NAG 337 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.492 ? covale ? covale3 B O4 NAG . B NAG 1 1_555 B C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.411 ? covale ? covale4 B O4 NAG . B NAG 2 1_555 B C1 BMA . B BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale5 B O3 BMA . B BMA 3 1_555 B C1 BMA . B BMA 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.41 ? covale ? covale6 B O2 BMA . B BMA 4 1_555 B C1 MAN . B MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.462 ? # _chem_comp.formula 'C8 H15 N O6' _chem_comp.formula_weight 221.208 _chem_comp.id NAG _chem_comp.mon_nstd_flag . _chem_comp.name 2-acetamido-2-deoxy-beta-D-glucopyranose _chem_comp.type 'd-saccharide, beta linking' _chem_comp.pdbx_synonyms N-acetyl-beta-D-glucosamine;2-acetamido-2-deoxy-beta-D-glucose;2-acetamido-2-deoxy-D-glucose;2-acetamido-2-deoxy-glucose;N-ACETYL-D-GLUCOSAMINE # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag C1 C2 NAG sing 382 n n C1 O1 NAG sing 383 n n C1 O5 NAG sing 384 n n C1 H1 NAG sing 385 n n C2 C3 NAG sing 386 n n C2 N2 NAG sing 387 n n C2 H2 NAG sing 388 n n C3 C4 NAG sing 389 n n C3 O3 NAG sing 390 n n C3 H3 NAG sing 391 n n C4 C5 NAG sing 392 n n C4 O4 NAG sing 393 n n C4 H4 NAG sing 394 n n C5 C6 NAG sing 395 n n C5 O5 NAG sing 396 n n C5 H5 NAG sing 397 n n C6 O6 NAG sing 398 n n C6 H61 NAG sing 399 n n C6 H62 NAG sing 400 n n C7 C8 NAG sing 401 n n C7 N2 NAG sing 402 n n C7 O7 NAG doub 403 n n C8 H81 NAG sing 404 n n C8 H82 NAG sing 405 n n C8 H83 NAG sing 406 n n N2 HN2 NAG sing 407 n n O1 HO1 NAG sing 408 n n O3 HO3 NAG sing 409 n n O4 HO4 NAG sing 410 n n O6 HO6 NAG sing 411 n n # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.identifier _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version NAG DGlcpNAcb 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1 NAG N-acetyl-b-D-glucopyranosamine 'COMMON NAME' GMML 1 NAG b-D-GlcpNAc 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1 NAG GlcNAc 'SNFG CARBOHYDRATE SYMBOL' GMML 1 # _atom_sites.entry_id 2JXR _atom_sites.fract_transf_matrix[1][1] 0.011534 _atom_sites.fract_transf_matrix[1][2] 0.006659 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013318 _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] 0.009058 _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 3 2Z3 A 1 327 327 2Z3 MOR . D 4 NAG A 1 337 337 NAG NAG . E 5 HOH A 1 501 501 HOH HOH . E 5 HOH A 2 502 502 HOH HOH . E 5 HOH A 3 503 503 HOH HOH . E 5 HOH A 4 505 505 HOH HOH . E 5 HOH A 5 510 510 HOH HOH . E 5 HOH A 6 512 512 HOH HOH . E 5 HOH A 7 514 514 HOH HOH . E 5 HOH A 8 515 515 HOH HOH . E 5 HOH A 9 516 516 HOH HOH . E 5 HOH A 10 517 517 HOH HOH . E 5 HOH A 11 522 522 HOH HOH . E 5 HOH A 12 523 523 HOH HOH . E 5 HOH A 13 524 524 HOH HOH . E 5 HOH A 14 525 525 HOH HOH . E 5 HOH A 15 526 526 HOH HOH . E 5 HOH A 16 527 527 HOH HOH . E 5 HOH A 17 529 529 HOH HOH . E 5 HOH A 18 532 532 HOH HOH . E 5 HOH A 19 533 533 HOH HOH . E 5 HOH A 20 534 534 HOH HOH . E 5 HOH A 21 535 535 HOH HOH . E 5 HOH A 22 537 537 HOH HOH . E 5 HOH A 23 538 538 HOH HOH . E 5 HOH A 24 540 540 HOH HOH . E 5 HOH A 25 543 543 HOH HOH . E 5 HOH A 26 544 544 HOH HOH . E 5 HOH A 27 546 546 HOH HOH . E 5 HOH A 28 547 547 HOH HOH . E 5 HOH A 29 548 548 HOH HOH . E 5 HOH A 30 549 549 HOH HOH . E 5 HOH A 31 553 553 HOH HOH . E 5 HOH A 32 555 555 HOH HOH . E 5 HOH A 33 557 557 HOH HOH . E 5 HOH A 34 558 558 HOH HOH . E 5 HOH A 35 559 559 HOH HOH . E 5 HOH A 36 561 561 HOH HOH . E 5 HOH A 37 562 562 HOH HOH . E 5 HOH A 38 563 563 HOH HOH . E 5 HOH A 39 566 566 HOH HOH . E 5 HOH A 40 571 571 HOH HOH . E 5 HOH A 41 572 572 HOH HOH . E 5 HOH A 42 573 573 HOH HOH . E 5 HOH A 43 574 574 HOH HOH . E 5 HOH A 44 576 576 HOH HOH . E 5 HOH A 45 577 577 HOH HOH . E 5 HOH A 46 578 578 HOH HOH . E 5 HOH A 47 579 579 HOH HOH . E 5 HOH A 48 580 580 HOH HOH . E 5 HOH A 49 581 581 HOH HOH . E 5 HOH A 50 582 582 HOH HOH . E 5 HOH A 51 583 583 HOH HOH . E 5 HOH A 52 584 584 HOH HOH . E 5 HOH A 53 602 602 HOH HOH . E 5 HOH A 54 605 605 HOH HOH . E 5 HOH A 55 606 606 HOH HOH . E 5 HOH A 56 610 610 HOH HOH . E 5 HOH A 57 611 611 HOH HOH . E 5 HOH A 58 616 616 HOH HOH . E 5 HOH A 59 617 617 HOH HOH . E 5 HOH A 60 619 619 HOH HOH . E 5 HOH A 61 621 621 HOH HOH . E 5 HOH A 62 622 622 HOH HOH . E 5 HOH A 63 623 623 HOH HOH . E 5 HOH A 64 624 624 HOH HOH . E 5 HOH A 65 626 626 HOH HOH . E 5 HOH A 66 629 629 HOH HOH . E 5 HOH A 67 631 631 HOH HOH . E 5 HOH A 68 632 632 HOH HOH . E 5 HOH A 69 633 633 HOH HOH . E 5 HOH A 70 634 634 HOH HOH . E 5 HOH A 71 635 635 HOH HOH . E 5 HOH A 72 639 639 HOH HOH . E 5 HOH A 73 640 640 HOH HOH . E 5 HOH A 74 642 642 HOH HOH . E 5 HOH A 75 643 643 HOH HOH . E 5 HOH A 76 644 644 HOH HOH . E 5 HOH A 77 645 645 HOH HOH . E 5 HOH A 78 648 648 HOH HOH . E 5 HOH A 79 649 649 HOH HOH . E 5 HOH A 80 650 650 HOH HOH . E 5 HOH A 81 653 653 HOH HOH . E 5 HOH A 82 655 655 HOH HOH . E 5 HOH A 83 656 656 HOH HOH . E 5 HOH A 84 657 657 HOH HOH . E 5 HOH A 85 658 658 HOH HOH . E 5 HOH A 86 660 660 HOH HOH . E 5 HOH A 87 661 661 HOH HOH . E 5 HOH A 88 662 662 HOH HOH . E 5 HOH A 89 663 663 HOH HOH . E 5 HOH A 90 664 664 HOH HOH . E 5 HOH A 91 665 665 HOH HOH . E 5 HOH A 92 666 666 HOH HOH . E 5 HOH A 93 667 667 HOH HOH . E 5 HOH A 94 673 673 HOH HOH . E 5 HOH A 95 675 675 HOH HOH . E 5 HOH A 96 676 676 HOH HOH . E 5 HOH A 97 677 677 HOH HOH . E 5 HOH A 98 679 679 HOH HOH . E 5 HOH A 99 680 680 HOH HOH . E 5 HOH A 100 683 683 HOH HOH . E 5 HOH A 101 686 686 HOH HOH . E 5 HOH A 102 690 690 HOH HOH . E 5 HOH A 103 691 691 HOH HOH . E 5 HOH A 104 694 694 HOH HOH . E 5 HOH A 105 695 695 HOH HOH . E 5 HOH A 106 696 696 HOH HOH . E 5 HOH A 107 697 697 HOH HOH . E 5 HOH A 108 698 698 HOH HOH . E 5 HOH A 109 699 699 HOH HOH . E 5 HOH A 110 700 700 HOH HOH . E 5 HOH A 111 701 701 HOH HOH . E 5 HOH A 112 702 702 HOH HOH . E 5 HOH A 113 703 703 HOH HOH . E 5 HOH A 114 704 704 HOH HOH . E 5 HOH A 115 705 705 HOH HOH . E 5 HOH A 116 706 706 HOH HOH . E 5 HOH A 117 707 707 HOH HOH . E 5 HOH A 118 708 708 HOH HOH . E 5 HOH A 119 709 709 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 C C1 NAG . . . D 4 5.179 64.227 21.575 1 157.91 ? C1 NAG 337 A 1 HETATM 2 C C2 NAG . . . D 4 5.331 65.651 21.129 1 48.87 ? C2 NAG 337 A 1 HETATM 3 C C3 NAG . . . D 4 4.692 66.124 19.917 1 68.45 ? C3 NAG 337 A 1 HETATM 4 C C4 NAG . . . D 4 3.711 65.274 19.218 1 48.6 ? C4 NAG 337 A 1 HETATM 5 C C5 NAG . . . D 4 3.192 64.106 20.018 1 36.88 ? C5 NAG 337 A 1 HETATM 6 C C6 NAG . . . D 4 2.954 62.787 19.238 1 157.91 ? C6 NAG 337 A 1 HETATM 7 C C7 NAG . . . D 4 7.439 65.204 22.118 1 105.66 ? C7 NAG 337 A 1 HETATM 8 C C8 NAG . . . D 4 7.698 65.942 23.392 1 49.66 ? C8 NAG 337 A 1 HETATM 9 N N2 NAG . . . D 4 6.782 66 21.196 1 53.9 ? N2 NAG 337 A 1 HETATM 10 O O3 NAG . . . D 4 5.581 66.71 18.933 1 66.2 ? O3 NAG 337 A 1 HETATM 11 O O4 NAG . . . D 4 2.647 66.05 18.637 1 56.14 ? O4 NAG 337 A 1 HETATM 12 O O5 NAG . . . D 4 3.989 63.583 21.138 1 114.72 ? O5 NAG 337 A 1 HETATM 13 O O6 NAG . . . D 4 2.882 61.79 20.262 1 41.69 ? O6 NAG 337 A 1 HETATM 14 O O7 NAG . . . D 4 7.737 64.051 21.879 1 43.27 ? O7 NAG 337 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 18 _model_server_stats.query_time_ms 308 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 14 #