data_3VQ1 # _model_server_result.job_id mgUfriX02oEDmeSLk3NOPA _model_server_result.datetime_utc '2024-11-28 19:10:06' _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 3vq1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":705}' # _entry.id 3VQ1 # _exptl.entry_id 3VQ1 _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 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 3VQ1 _cell.length_a 77.16 _cell.length_b 150.519 _cell.length_c 181.847 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3VQ1 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,M,N,O,P,Q _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 ? 4 H N N ? 4 K N N # _pdbx_entity_branch.entity_id 3 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 3 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 NAG _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order 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 3 n E NAG 1 E 1 NAG A 800 NAG 3 n E NAG 2 E 2 NAG A 801 NAG 3 n F NAG 1 F 1 NAG A 802 NAG 3 n F NAG 2 F 2 NAG A 803 NAG 3 n G NAG 1 G 1 NAG B 800 NAG 3 n G NAG 2 G 2 NAG B 801 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 7 A CYS 28 1_555 A SG CYS 18 A CYS 39 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf2 A SG CYS 259 A CYS 280 1_555 A SG CYS 283 A CYS 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf3 A SG CYS 367 A CYS 388 1_555 A SG CYS 368 A CYS 389 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? disulf ? disulf4 A SG CYS 559 A CYS 580 1_555 A SG CYS 585 A CYS 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf5 A SG CYS 561 A CYS 582 1_555 A SG CYS 604 A CYS 625 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf6 B SG CYS 9 C CYS 25 1_555 B SG CYS 35 C CYS 51 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf7 B SG CYS 21 C CYS 37 1_555 B SG CYS 132 C CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? disulf ? disulf8 B SG CYS 79 C CYS 95 1_555 B SG CYS 89 C CYS 105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? disulf ? disulf9 C SG CYS 7 B CYS 28 1_555 C SG CYS 18 B CYS 39 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf10 C SG CYS 259 B CYS 280 1_555 C SG CYS 283 B CYS 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? disulf ? disulf11 C SG CYS 367 B CYS 388 1_555 C SG CYS 368 B CYS 389 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? disulf ? disulf12 C SG CYS 559 B CYS 580 1_555 C SG CYS 585 B CYS 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf13 C SG CYS 561 B CYS 582 1_555 C SG CYS 604 B CYS 625 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf14 D SG CYS 9 D CYS 25 1_555 D SG CYS 35 D CYS 51 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf15 D SG CYS 21 D CYS 37 1_555 D SG CYS 132 D CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf16 D SG CYS 79 D CYS 95 1_555 D SG CYS 89 D CYS 105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? covale ? covale1 A ND2 ASN 183 A ASN 204 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.367 ? covale ? covale2 A ND2 ASN 503 A ASN 524 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.4 ? covale ? covale3 I C1 LP4 . C LP4 300 1_555 J O6 LP5 . C LP5 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale4 C ND2 ASN 503 B ASN 524 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale5 C ND2 ASN 551 B ASN 572 1_555 K C1 NAG . B NAG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.456 ? covale ? covale6 L C1 LP4 . D LP4 300 1_555 M O6 LP5 . D LP5 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale7 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale8 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale9 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? # _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 465 n n C1 O1 NAG sing 466 n n C1 O5 NAG sing 467 n n C1 H1 NAG sing 468 n n C2 C3 NAG sing 469 n n C2 N2 NAG sing 470 n n C2 H2 NAG sing 471 n n C3 C4 NAG sing 472 n n C3 O3 NAG sing 473 n n C3 H3 NAG sing 474 n n C4 C5 NAG sing 475 n n C4 O4 NAG sing 476 n n C4 H4 NAG sing 477 n n C5 C6 NAG sing 478 n n C5 O5 NAG sing 479 n n C5 H5 NAG sing 480 n n C6 O6 NAG sing 481 n n C6 H61 NAG sing 482 n n C6 H62 NAG sing 483 n n C7 C8 NAG sing 484 n n C7 N2 NAG sing 485 n n C7 O7 NAG doub 486 n n C8 H81 NAG sing 487 n n C8 H82 NAG sing 488 n n C8 H83 NAG sing 489 n n N2 HN2 NAG sing 490 n n O1 HO1 NAG sing 491 n n O3 HO3 NAG sing 492 n n O4 HO4 NAG sing 493 n n O6 HO6 NAG sing 494 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 3VQ1 _atom_sites.fract_transf_matrix[1][1] 0.01296 _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] 0.006644 _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] 0.005499 _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 H 4 NAG A 1 705 804 NAG NAG . I 5 LP4 C 1 300 300 LP4 LP4 . J 6 LP5 C 1 301 301 LP5 LP5 . K 4 NAG B 1 802 802 NAG NAG . L 5 LP4 D 1 300 300 LP4 LP4 . M 6 LP5 D 1 301 301 LP5 LP5 . N 7 HOH A 1 801 4 HOH HOH . N 7 HOH A 2 802 6 HOH HOH . N 7 HOH A 3 803 8 HOH HOH . N 7 HOH A 4 804 10 HOH HOH . N 7 HOH A 5 805 12 HOH HOH . N 7 HOH A 6 806 15 HOH HOH . N 7 HOH A 7 807 17 HOH HOH . N 7 HOH A 8 808 19 HOH HOH . N 7 HOH A 9 809 20 HOH HOH . N 7 HOH A 10 810 25 HOH HOH . N 7 HOH A 11 811 26 HOH HOH . N 7 HOH A 12 812 27 HOH HOH . N 7 HOH A 13 813 29 HOH HOH . N 7 HOH A 14 814 30 HOH HOH . N 7 HOH A 15 815 32 HOH HOH . O 7 HOH C 1 401 22 HOH HOH . O 7 HOH C 2 402 23 HOH HOH . O 7 HOH C 3 403 24 HOH HOH . O 7 HOH C 4 404 36 HOH HOH . P 7 HOH B 1 901 1 HOH HOH . P 7 HOH B 2 902 2 HOH HOH . P 7 HOH B 3 903 3 HOH HOH . P 7 HOH B 4 904 5 HOH HOH . P 7 HOH B 5 905 7 HOH HOH . P 7 HOH B 6 906 9 HOH HOH . P 7 HOH B 7 907 11 HOH HOH . P 7 HOH B 8 908 13 HOH HOH . P 7 HOH B 9 909 14 HOH HOH . P 7 HOH B 10 910 16 HOH HOH . P 7 HOH B 11 911 18 HOH HOH . P 7 HOH B 12 912 21 HOH HOH . P 7 HOH B 13 913 28 HOH HOH . P 7 HOH B 14 914 31 HOH HOH . P 7 HOH B 15 915 33 HOH HOH . P 7 HOH B 16 916 35 HOH HOH . P 7 HOH B 17 917 37 HOH HOH . Q 7 HOH D 1 401 34 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 . . . H 4 -2.887 3.797 38.969 1 66.57 ? C1 NAG 705 A 1 HETATM 2 C C2 NAG . . . H 4 -2.828 4.883 37.891 1 64.51 ? C2 NAG 705 A 1 HETATM 3 C C3 NAG . . . H 4 -1.364 5.217 37.605 1 66.64 ? C3 NAG 705 A 1 HETATM 4 C C4 NAG . . . H 4 -0.551 5.5 38.868 1 71.56 ? C4 NAG 705 A 1 HETATM 5 C C5 NAG . . . H 4 -0.802 4.443 39.96 1 80.29 ? C5 NAG 705 A 1 HETATM 6 C C6 NAG . . . H 4 -0.182 4.854 41.301 1 86.39 ? C6 NAG 705 A 1 HETATM 7 C C7 NAG . . . H 4 -4.284 5.207 35.894 1 57.58 ? C7 NAG 705 A 1 HETATM 8 C C8 NAG . . . H 4 -4.849 4.605 34.645 1 50.88 ? C8 NAG 705 A 1 HETATM 9 N N2 NAG . . . H 4 -3.477 4.446 36.656 1 59.48 ? N2 NAG 705 A 1 HETATM 10 O O3 NAG . . . H 4 -1.283 6.332 36.757 1 67.31 ? O3 NAG 705 A 1 HETATM 11 O O4 NAG . . . H 4 0.819 5.526 38.519 1 64.48 ? O4 NAG 705 A 1 HETATM 12 O O5 NAG . . . H 4 -2.193 4.193 40.143 1 73.31 ? O5 NAG 705 A 1 HETATM 13 O O6 NAG . . . H 4 1.232 4.77 41.25 1 87.93 ? O6 NAG 705 A 1 HETATM 14 O O7 NAG . . . H 4 -4.596 6.366 36.146 1 61.51 ? O7 NAG 705 A 1 # _model_server_stats.io_time_ms 29 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 327 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 14 #