data_5VCS # _model_server_result.job_id nUwbQX67mY80rya-7z1Hiw _model_server_result.datetime_utc '2024-11-17 02:38:49' _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 5vcs # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":506}' # _entry.id 5VCS # _exptl.entry_id 5VCS _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 3 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _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 90 _cell.entry_id 5VCS _cell.length_a 46.28 _cell.length_b 129.16 _cell.length_c 175.8 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5VCS _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 2 21 21' # _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,L _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 E N N ? 3 I N 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 BMA NAG C1 O1 . O4 HO4 . sing 2 ? 2 3 2 MAN BMA C1 O1 . O3 HO3 . sing 3 ? 2 4 3 NAG MAN C1 O1 . O2 HO2 . sing 4 ? 2 5 2 MAN BMA 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 2 n C NAG 1 C 1 NAG A 504 NAG 2 n C BMA 2 C 2 BMA A 502 BMA 2 n C MAN 3 C 3 MAN A 501 MAN 2 n C NAG 4 C 4 NAG A 500 NAG 2 n C MAN 5 C 5 MAN A 503 MAN 2 n D NAG 1 D 1 NAG B 504 NAG 2 n D BMA 2 D 2 BMA B 502 BMA 2 n D MAN 3 D 3 MAN B 501 MAN 2 n D NAG 4 D 4 NAG B 500 NAG 2 n D MAN 5 D 5 MAN B 503 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 168 A CYS 196 1_555 A SG CYS 182 A CYS 210 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf2 A SG CYS 255 A CYS 283 1_555 A SG CYS 258 A CYS 286 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf3 A SG CYS 306 A CYS 334 1_555 A SG CYS 329 A CYS 357 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf4 A SG CYS 311 A CYS 339 1_555 A SG CYS 412 A CYS 440 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf5 B SG CYS 168 B CYS 196 1_555 B SG CYS 182 B CYS 210 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf6 B SG CYS 255 B CYS 283 1_555 B SG CYS 258 B CYS 286 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf7 B SG CYS 306 B CYS 334 1_555 B SG CYS 329 B CYS 357 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.04 ? disulf ? disulf8 B SG CYS 311 B CYS 339 1_555 B SG CYS 412 B CYS 440 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? covale ? covale1 A ND2 ASN 58 A ASN 86 1_555 E C1 NAG . A NAG 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale2 B ND2 ASN 58 B ASN 86 1_555 I C1 NAG . B NAG 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale3 B NH2 ARG 398 B ARG 426 1_555 D O6 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.297 ? covale ? covale4 C O4 NAG . C NAG 1 1_555 C C1 BMA . C BMA 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale5 C O3 BMA . C BMA 2 1_555 C C1 MAN . C MAN 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale6 C O6 BMA . C BMA 2 1_555 C C1 MAN . C MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale7 C O2 MAN . C MAN 3 1_555 C C1 NAG . C NAG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale8 D O4 NAG . D NAG 1 1_555 D C1 BMA . D BMA 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.462 ? covale ? covale9 D O3 BMA . D BMA 2 1_555 D C1 MAN . D MAN 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale10 D O6 BMA . D BMA 2 1_555 D C1 MAN . D MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale11 D O2 MAN . D MAN 3 1_555 D C1 NAG . D NAG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? # _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 294 n n C1 O1 NAG sing 295 n n C1 O5 NAG sing 296 n n C1 H1 NAG sing 297 n n C2 C3 NAG sing 298 n n C2 N2 NAG sing 299 n n C2 H2 NAG sing 300 n n C3 C4 NAG sing 301 n n C3 O3 NAG sing 302 n n C3 H3 NAG sing 303 n n C4 C5 NAG sing 304 n n C4 O4 NAG sing 305 n n C4 H4 NAG sing 306 n n C5 C6 NAG sing 307 n n C5 O5 NAG sing 308 n n C5 H5 NAG sing 309 n n C6 O6 NAG sing 310 n n C6 H61 NAG sing 311 n n C6 H62 NAG sing 312 n n C7 C8 NAG sing 313 n n C7 N2 NAG sing 314 n n C7 O7 NAG doub 315 n n C8 H81 NAG sing 316 n n C8 H82 NAG sing 317 n n C8 H83 NAG sing 318 n n N2 HN2 NAG sing 319 n n O1 HO1 NAG sing 320 n n O3 HO3 NAG sing 321 n n O4 HO4 NAG sing 322 n n O6 HO6 NAG sing 323 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 5VCS _atom_sites.fract_transf_matrix[1][1] 0.021608 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007742 _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] 0.005688 _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 3 NAG A 1 506 600 NAG NAG . F 4 DMS A 1 507 700 DMS DMS . G 4 DMS A 1 508 701 DMS DMS . H 4 DMS A 1 509 702 DMS DMS . I 3 NAG B 1 506 600 NAG NAG . J 5 PEG B 1 507 703 PEG PEG . K 6 HOH A 1 601 8 HOH HOH . K 6 HOH A 2 602 64 HOH HOH . K 6 HOH A 3 603 111 HOH HOH . K 6 HOH A 4 604 2 HOH HOH . K 6 HOH A 5 605 80 HOH HOH . K 6 HOH A 6 606 38 HOH HOH . K 6 HOH A 7 607 1 HOH HOH . K 6 HOH A 8 608 14 HOH HOH . K 6 HOH A 9 609 52 HOH HOH . K 6 HOH A 10 610 21 HOH HOH . K 6 HOH A 11 611 26 HOH HOH . K 6 HOH A 12 612 24 HOH HOH . K 6 HOH A 13 613 44 HOH HOH . K 6 HOH A 14 614 17 HOH HOH . K 6 HOH A 15 615 28 HOH HOH . K 6 HOH A 16 616 51 HOH HOH . K 6 HOH A 17 617 6 HOH HOH . K 6 HOH A 18 618 16 HOH HOH . K 6 HOH A 19 619 48 HOH HOH . K 6 HOH A 20 620 12 HOH HOH . K 6 HOH A 21 621 55 HOH HOH . K 6 HOH A 22 622 105 HOH HOH . K 6 HOH A 23 623 33 HOH HOH . K 6 HOH A 24 624 20 HOH HOH . K 6 HOH A 25 625 67 HOH HOH . K 6 HOH A 26 626 91 HOH HOH . K 6 HOH A 27 627 68 HOH HOH . K 6 HOH A 28 628 56 HOH HOH . K 6 HOH A 29 629 54 HOH HOH . K 6 HOH A 30 630 50 HOH HOH . K 6 HOH A 31 631 78 HOH HOH . K 6 HOH A 32 632 47 HOH HOH . K 6 HOH A 33 633 65 HOH HOH . K 6 HOH A 34 634 104 HOH HOH . K 6 HOH A 35 635 66 HOH HOH . K 6 HOH A 36 636 34 HOH HOH . K 6 HOH A 37 637 60 HOH HOH . K 6 HOH A 38 638 100 HOH HOH . K 6 HOH A 39 639 79 HOH HOH . K 6 HOH A 40 640 4 HOH HOH . K 6 HOH A 41 641 57 HOH HOH . K 6 HOH A 42 642 53 HOH HOH . K 6 HOH A 43 643 85 HOH HOH . K 6 HOH A 44 644 41 HOH HOH . K 6 HOH A 45 645 112 HOH HOH . K 6 HOH A 46 646 87 HOH HOH . K 6 HOH A 47 647 98 HOH HOH . K 6 HOH A 48 648 86 HOH HOH . K 6 HOH A 49 649 22 HOH HOH . K 6 HOH A 50 650 103 HOH HOH . K 6 HOH A 51 651 89 HOH HOH . K 6 HOH A 52 652 19 HOH HOH . K 6 HOH A 53 653 36 HOH HOH . K 6 HOH A 54 654 23 HOH HOH . K 6 HOH A 55 655 93 HOH HOH . K 6 HOH A 56 656 58 HOH HOH . K 6 HOH A 57 657 29 HOH HOH . K 6 HOH A 58 658 95 HOH HOH . K 6 HOH A 59 659 69 HOH HOH . K 6 HOH A 60 660 92 HOH HOH . L 6 HOH B 1 601 27 HOH HOH . L 6 HOH B 2 602 35 HOH HOH . L 6 HOH B 3 603 40 HOH HOH . L 6 HOH B 4 604 10 HOH HOH . L 6 HOH B 5 605 5 HOH HOH . L 6 HOH B 6 606 59 HOH HOH . L 6 HOH B 7 607 7 HOH HOH . L 6 HOH B 8 608 43 HOH HOH . L 6 HOH B 9 609 3 HOH HOH . L 6 HOH B 10 610 72 HOH HOH . L 6 HOH B 11 611 99 HOH HOH . L 6 HOH B 12 612 11 HOH HOH . L 6 HOH B 13 613 101 HOH HOH . L 6 HOH B 14 614 18 HOH HOH . L 6 HOH B 15 615 83 HOH HOH . L 6 HOH B 16 616 30 HOH HOH . L 6 HOH B 17 617 49 HOH HOH . L 6 HOH B 18 618 108 HOH HOH . L 6 HOH B 19 619 102 HOH HOH . L 6 HOH B 20 620 62 HOH HOH . L 6 HOH B 21 621 39 HOH HOH . L 6 HOH B 22 622 32 HOH HOH . L 6 HOH B 23 623 109 HOH HOH . L 6 HOH B 24 624 94 HOH HOH . L 6 HOH B 25 625 42 HOH HOH . L 6 HOH B 26 626 61 HOH HOH . L 6 HOH B 27 627 73 HOH HOH . L 6 HOH B 28 628 106 HOH HOH . L 6 HOH B 29 629 82 HOH HOH . L 6 HOH B 30 630 37 HOH HOH . L 6 HOH B 31 631 13 HOH HOH . L 6 HOH B 32 632 84 HOH HOH . L 6 HOH B 33 633 63 HOH HOH . L 6 HOH B 34 634 15 HOH HOH . L 6 HOH B 35 635 9 HOH HOH . L 6 HOH B 36 636 81 HOH HOH . L 6 HOH B 37 637 31 HOH HOH . L 6 HOH B 38 638 110 HOH HOH . L 6 HOH B 39 639 76 HOH HOH . L 6 HOH B 40 640 45 HOH HOH . L 6 HOH B 41 641 88 HOH HOH . L 6 HOH B 42 642 25 HOH HOH . L 6 HOH B 43 643 70 HOH HOH . L 6 HOH B 44 644 74 HOH HOH . L 6 HOH B 45 645 75 HOH HOH . L 6 HOH B 46 646 96 HOH HOH . L 6 HOH B 47 647 71 HOH HOH . L 6 HOH B 48 648 107 HOH HOH . L 6 HOH B 49 649 97 HOH HOH . L 6 HOH B 50 650 46 HOH HOH . L 6 HOH B 51 651 90 HOH HOH . L 6 HOH B 52 652 77 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 . . . I 3 -41.719 -11.93 42.915 0.9 48.08 ? C1 NAG 506 B 1 HETATM 2 C C2 NAG . . . I 3 -41.489 -10.423 43.051 0.9 50.54 ? C2 NAG 506 B 1 HETATM 3 C C3 NAG . . . I 3 -42.033 -9.953 44.395 0.9 51.86 ? C3 NAG 506 B 1 HETATM 4 C C4 NAG . . . I 3 -43.491 -10.357 44.555 0.9 51.86 ? C4 NAG 506 B 1 HETATM 5 C C5 NAG . . . I 3 -43.611 -11.864 44.37 0.9 51.45 ? C5 NAG 506 B 1 HETATM 6 C C6 NAG . . . I 3 -45.076 -12.271 44.475 0.9 52.79 ? C6 NAG 506 B 1 HETATM 7 C C7 NAG . . . I 3 -39.604 -8.96 42.553 0.9 51.87 ? C7 NAG 506 B 1 HETATM 8 C C8 NAG . . . I 3 -38.115 -8.796 42.478 0.9 51.76 ? C8 NAG 506 B 1 HETATM 9 N N2 NAG . . . I 3 -40.069 -10.132 42.979 0.9 51.15 ? N2 NAG 506 B 1 HETATM 10 O O3 NAG . . . I 3 -41.92 -8.528 44.491 0.9 52.19 ? O3 NAG 506 B 1 HETATM 11 O O4 NAG . . . I 3 -43.943 -10 45.866 0.9 53.16 ? O4 NAG 506 B 1 HETATM 12 O O5 NAG . . . I 3 -43.106 -12.237 43.086 0.9 50.25 ? O5 NAG 506 B 1 HETATM 13 O O6 NAG . . . I 3 -45.19 -13.689 44.313 0.9 53.73 ? O6 NAG 506 B 1 HETATM 14 O O7 NAG . . . I 3 -40.358 -8.055 42.237 0.9 52.16 ? O7 NAG 506 B 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 287 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 14 #