data_4NDZ # _model_server_result.job_id LLjHMYyyk3-lXowxYXIIgw _model_server_result.datetime_utc '2024-10-19 15:34:03' _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 4ndz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"Y","auth_seq_id":2011}' # _entry.id 4NDZ # _exptl.entry_id 4NDZ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 139.109 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description P-NITROPHENOL _entity.pdbx_number_of_molecules 4 _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 4NDZ _cell.length_a 155.72 _cell.length_b 170.69 _cell.length_c 183.96 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4NDZ _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # 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 trimeric 3 author_and_software_defined_assembly 1 PISA trimeric 3 author_and_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,G,H,I,J,Q,R,S,T,U 1 1 D,E,F,K,L,M,N,O,P,V,W,X,Y,Z 2 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 ? 5 R N N ? 5 T N N ? 5 W N N ? 5 Y N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 2 oligosaccharide 3 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 GNS BDP C1 O1 . O4 HO4 . sing 2 ? 2 3 2 IDR GNS C1 O1 . O4 HO4 . sing 3 ? 2 4 3 GNS IDR C1 O1 . O4 HO4 . sing 4 ? 2 5 4 BDP GNS C1 O1 . O4 HO4 . sing 5 ? 2 6 5 NDG BDP C1 O1 . O4 HO4 . sing 6 ? 2 7 6 BDP NDG C1 O1 . O4 HO4 . sing 7 ? 3 2 1 GLC GLC C1 O1 . O4 HO4 . 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 G BDP 1 G 1 BDP A 3007 BDP 2 n G GNS 2 G 2 GNS A 3006 GNS 2 n G IDR 3 G 3 IDR A 3005 IDS 2 n G GNS 4 G 4 GNS A 3004 GNS 2 n G BDP 5 G 5 BDP A 3003 BDP 2 n G NDG 6 G 6 NDG A 3002 NDG 2 n G BDP 7 G 7 BDP A 3001 BDP 3 n H GLC 1 H 1 GLC B 2002 GLC 3 n H GLC 2 H 2 GLC B 2001 GLC 2 n I BDP 1 I 1 BDP B 3007 BDP 2 n I GNS 2 I 2 GNS B 3006 GNS 2 n I IDR 3 I 3 IDR B 3005 IDS 2 n I GNS 4 I 4 GNS B 3004 GNS 2 n I BDP 5 I 5 BDP B 3003 BDP 2 n I NDG 6 I 6 NDG B 3002 NDG 2 n I BDP 7 I 7 BDP B 3001 BDP 3 n J GLC 1 J 1 GLC C 2002 GLC 3 n J GLC 2 J 2 GLC C 2001 GLC 3 n K GLC 1 K 1 GLC D 2002 GLC 3 n K GLC 2 K 2 GLC D 2001 GLC 2 n L BDP 1 L 1 BDP D 3007 BDP 2 n L GNS 2 L 2 GNS D 3006 GNS 2 n L IDR 3 L 3 IDR D 3005 IDS 2 n L GNS 4 L 4 GNS D 3004 GNS 2 n L BDP 5 L 5 BDP D 3003 BDP 2 n L NDG 6 L 6 NDG D 3002 NDG 2 n L BDP 7 L 7 BDP D 3001 BDP 3 n M GLC 1 M 1 GLC E 2002 GLC 3 n M GLC 2 M 2 GLC E 2001 GLC 2 n N BDP 1 N 1 BDP E 3007 BDP 2 n N GNS 2 N 2 GNS E 3006 GNS 2 n N IDR 3 N 3 IDR E 3005 IDS 2 n N GNS 4 N 4 GNS E 3004 GNS 2 n N BDP 5 N 5 BDP E 3003 BDP 2 n N NDG 6 N 6 NDG E 3002 NDG 2 n N BDP 7 N 7 BDP E 3001 BDP 3 n O GLC 1 O 1 GLC F 2002 GLC 3 n O GLC 2 O 2 GLC F 2001 GLC 2 n P BDP 1 P 1 BDP F 3007 BDP 2 n P GNS 2 P 2 GNS F 3006 GNS 2 n P IDR 3 P 3 IDR F 3005 IDS 2 n P GNS 4 P 4 GNS F 3004 GNS 2 n P BDP 5 P 5 BDP F 3003 BDP 2 n P NDG 6 P 6 NDG F 3002 NDG 2 n P BDP 7 P 7 BDP F 3001 BDP # 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 503 A CYS 1201 1_555 A SG CYS 511 A CYS 1209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf2 A SG CYS 524 A CYS 1222 1_555 A SG CYS 530 A CYS 1228 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf3 B SG CYS 503 B CYS 1201 1_555 B SG CYS 511 B CYS 1209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf4 B SG CYS 524 B CYS 1222 1_555 B SG CYS 530 B CYS 1228 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf5 C SG CYS 503 C CYS 1201 1_555 C SG CYS 511 C CYS 1209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf6 C SG CYS 524 C CYS 1222 1_555 C SG CYS 530 C CYS 1228 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf7 D SG CYS 503 D CYS 1201 1_555 D SG CYS 511 D CYS 1209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf8 D SG CYS 524 D CYS 1222 1_555 D SG CYS 530 D CYS 1228 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf9 E SG CYS 503 E CYS 1201 1_555 E SG CYS 511 E CYS 1209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf10 E SG CYS 524 E CYS 1222 1_555 E SG CYS 530 E CYS 1228 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf11 F SG CYS 503 F CYS 1201 1_555 F SG CYS 511 F CYS 1209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf12 F SG CYS 524 F CYS 1222 1_555 F SG CYS 530 F CYS 1228 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? covale ? covale1 R OH NPO . A NPO 2011 1_555 G C1 BDP . G BDP 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale2 T OH NPO . B NPO 2011 1_555 I C1 BDP . I BDP 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale3 W OH NPO . D NPO 2011 1_555 L C1 BDP . L BDP 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale4 Y OH NPO . E NPO 2011 1_555 N C1 BDP . N BDP 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale5 G O4 BDP . G BDP 1 1_555 G C1 GNS . G GNS 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale6 G O4 GNS . G GNS 2 1_555 G C1 IDR . G IDR 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale7 G O4 IDR . G IDR 3 1_555 G C1 GNS . G GNS 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale8 G O4 GNS . G GNS 4 1_555 G C1 BDP . G BDP 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale9 G O4 BDP . G BDP 5 1_555 G C1 NDG . G NDG 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale10 G O4 NDG . G NDG 6 1_555 G C1 BDP . G BDP 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale11 H O4 GLC . H GLC 1 1_555 H C1 GLC . H GLC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale12 I O4 BDP . I BDP 1 1_555 I C1 GNS . I GNS 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale13 I O4 GNS . I GNS 2 1_555 I C1 IDR . I IDR 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale14 I O4 IDR . I IDR 3 1_555 I C1 GNS . I GNS 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale15 I O4 GNS . I GNS 4 1_555 I C1 BDP . I BDP 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale16 I O4 BDP . I BDP 5 1_555 I C1 NDG . I NDG 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale17 I O4 NDG . I NDG 6 1_555 I C1 BDP . I BDP 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale18 J O4 GLC . J GLC 1 1_555 J C1 GLC . J GLC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale19 K O4 GLC . K GLC 1 1_555 K C1 GLC . K GLC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale20 L O4 BDP . L BDP 1 1_555 L C1 GNS . L GNS 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale21 L O4 GNS . L GNS 2 1_555 L C1 IDR . L IDR 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale22 L O4 IDR . L IDR 3 1_555 L C1 GNS . L GNS 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale23 L O4 GNS . L GNS 4 1_555 L C1 BDP . L BDP 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale24 L O4 BDP . L BDP 5 1_555 L C1 NDG . L NDG 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale25 L O4 NDG . L NDG 6 1_555 L C1 BDP . L BDP 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale26 M O4 GLC . M GLC 1 1_555 M C1 GLC . M GLC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale27 N O4 BDP . N BDP 1 1_555 N C1 GNS . N GNS 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale28 N O4 GNS . N GNS 2 1_555 N C1 IDR . N IDR 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale29 N O4 IDR . N IDR 3 1_555 N C1 GNS . N GNS 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale30 N O4 GNS . N GNS 4 1_555 N C1 BDP . N BDP 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale31 N O4 BDP . N BDP 5 1_555 N C1 NDG . N NDG 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale32 N O4 NDG . N NDG 6 1_555 N C1 BDP . N BDP 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale33 O O4 GLC . O GLC 1 1_555 O C1 GLC . O GLC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale34 P O4 BDP . P BDP 1 1_555 P C1 GNS . P GNS 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale35 P O4 GNS . P GNS 2 1_555 P C1 IDR . P IDR 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale36 P O4 IDR . P IDR 3 1_555 P C1 GNS . P GNS 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale37 P O4 GNS . P GNS 4 1_555 P C1 BDP . P BDP 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale38 P O4 BDP . P BDP 5 1_555 P C1 NDG . P NDG 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale39 P O4 NDG . P NDG 6 1_555 P C1 BDP . P BDP 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? # _chem_comp.formula 'C6 H5 N O3' _chem_comp.formula_weight 139.109 _chem_comp.id NPO _chem_comp.mon_nstd_flag . _chem_comp.name P-NITROPHENOL _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 NPO doub 408 n y C1 C6 NPO sing 409 n y C1 N1 NPO sing 410 n n C2 C3 NPO sing 411 n y C2 H2 NPO sing 412 n n C3 C4 NPO doub 413 n y C3 H3 NPO sing 414 n n C4 C5 NPO sing 415 n y C4 OH NPO sing 416 n n C5 C6 NPO doub 417 n y C5 H5 NPO sing 418 n n C6 H6 NPO sing 419 n n OH HO NPO sing 420 n n N1 O2 NPO sing 421 n n N1 O3 NPO doub 422 n n # _atom_sites.entry_id 4NDZ _atom_sites.fract_transf_matrix[1][1] 0.006422 _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] 0.005859 _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] 0.005436 _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 Q 4 A3P A 1 2003 2003 A3P A3P . R 5 NPO A 1 2011 3008 NPO NPO . S 4 A3P B 1 2003 2003 A3P A3P . T 5 NPO B 1 2011 3008 NPO NPO . U 4 A3P C 1 2003 2003 A3P A3P . V 4 A3P D 1 2003 2003 A3P A3P . W 5 NPO D 1 2011 3008 NPO NPO . X 4 A3P E 1 2003 2003 A3P A3P . Y 5 NPO E 1 2011 3008 NPO NPO . Z 4 A3P F 1 2003 2003 A3P A3P . # 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 NPO . . . Y 5 40.106 34.469 112.907 1 169.07 ? C1 NPO 2011 E 1 HETATM 2 C C2 NPO . . . Y 5 40.683 35.711 112.642 1 175.81 ? C2 NPO 2011 E 1 HETATM 3 C C3 NPO . . . Y 5 41.046 36.542 113.693 1 180.4 ? C3 NPO 2011 E 1 HETATM 4 C C4 NPO . . . Y 5 40.837 36.145 115 1 185.11 ? C4 NPO 2011 E 1 HETATM 5 C C5 NPO . . . Y 5 40.266 34.916 115.266 1 183.57 ? C5 NPO 2011 E 1 HETATM 6 C C6 NPO . . . Y 5 39.897 34.075 114.226 1 172.89 ? C6 NPO 2011 E 1 HETATM 7 O OH NPO . . . Y 5 41.198 36.973 116.042 1 189.84 ? OH NPO 2011 E 1 HETATM 8 N N1 NPO . . . Y 5 39.726 33.599 111.837 1 165.95 ? N1 NPO 2011 E 1 HETATM 9 O O2 NPO . . . Y 5 39.912 33.957 110.602 1 157.97 ? O2 NPO 2011 E 1 HETATM 10 O O3 NPO . . . Y 5 39.221 32.516 112.091 1 169.15 ? O3 NPO 2011 E 1 # _model_server_stats.io_time_ms 62 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 48 _model_server_stats.query_time_ms 357 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 10 #