data_4KVN # _model_server_result.job_id kk4PDRk-JizXAIK_9Ipmyw _model_server_result.datetime_utc '2024-10-17 21:56:49' _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 4kvn # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":604}' # _entry.id 4KVN # _exptl.entry_id 4KVN _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 6 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 5 _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 4KVN _cell.length_a 204.37 _cell.length_b 204.37 _cell.length_c 204.37 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4KVN _symmetry.cell_setting ? _symmetry.Int_Tables_number 199 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 21 3' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details nonameric _pdbx_struct_assembly.oligomeric_count 9 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 # 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' 7_454 -z-1/2,-x,y-1/2 0 0 -1 -1 0 0 0 1 0 -102.185 0 -102.185 3 'crystal symmetry operation' 10_554 -y,z+1/2,-x-1/2 0 -1 0 0 0 1 -1 0 0 0 102.185 -102.185 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 6 G N N ? 6 H N N ? 6 I N N ? 6 J N N ? 6 K N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 4 oligosaccharide 5 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 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 4 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 5 2 1 NAG NAG 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 4 n D NAG 1 B 1 NAG A 9032 NAG 4 n D NAG 2 B 2 NAG A 8032 NAG 4 n D BMA 3 B 3 BMA A 7032 BMA 4 n E NAG 1 C 1 NAG A 9159 NAG 4 n E NAG 2 C 2 NAG A 8159 NAG 4 n E BMA 3 C 3 BMA A 7159 BMA 5 n F NAG 1 D 1 NAG A 9240 NAG 5 n F NAG 2 D 2 NAG A 8240 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 8 A CYS 30 1_555 A SG CYS 460 A CYS 482 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf2 A SG CYS 46 A CYS 68 1_555 A SG CYS 271 A CYS 293 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? disulf ? disulf3 A SG CYS 58 A CYS 80 1_555 A SG CYS 70 A CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf4 A SG CYS 91 A CYS 113 1_555 A SG CYS 133 A CYS 155 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf5 A SG CYS 275 A CYS 297 1_555 A SG CYS 299 A CYS 321 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? disulf ? disulf6 A SG CYS 467 A CYS 489 1_555 A SG CYS 471 A CYS 493 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf7 B SG CYS 21 H CYS 22 1_555 B SG CYS 95 H CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf8 B SG CYS 151 H CYS 152 1_555 B SG CYS 207 H CYS 208 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf9 C SG CYS 22 L CYS 23 1_555 C SG CYS 87 L CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? disulf ? disulf10 C SG CYS 135 L CYS 134 1_555 C SG CYS 195 L CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? covale ? covale1 A ND2 ASN 32 A ASN 54 1_555 D C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.429 ? covale ? covale2 A ND2 ASN 57 A ASN 79 1_555 G C1 NAG . A NAG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale3 A ND2 ASN 120 A ASN 142 1_555 H C1 NAG . A NAG 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale4 A ND2 ASN 127 A ASN 149 1_555 I C1 NAG . A NAG 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.429 ? covale ? covale5 A ND2 ASN 159 A ASN 181 1_555 E C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.399 ? covale ? covale6 A ND2 ASN 240 A ASN 262 1_555 F C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale7 A ND2 ASN 279 A ASN 301 1_555 J C1 NAG . A NAG 612 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale8 A ND2 ASN 477 A ASN 499 1_555 K C1 NAG . A NAG 613 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale9 D O4 NAG . B NAG 1 1_555 D C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.412 ? covale ? covale10 D O4 NAG . B NAG 2 1_555 D C1 BMA . B BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale11 E O4 NAG . C NAG 1 1_555 E C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.301 ? covale ? covale12 E O4 NAG . C NAG 2 1_555 E C1 BMA . C BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale13 F O4 NAG . D NAG 1 1_555 F C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.419 ? # _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 261 n n C1 O1 NAG sing 262 n n C1 O5 NAG sing 263 n n C1 H1 NAG sing 264 n n C2 C3 NAG sing 265 n n C2 N2 NAG sing 266 n n C2 H2 NAG sing 267 n n C3 C4 NAG sing 268 n n C3 O3 NAG sing 269 n n C3 H3 NAG sing 270 n n C4 C5 NAG sing 271 n n C4 O4 NAG sing 272 n n C4 H4 NAG sing 273 n n C5 C6 NAG sing 274 n n C5 O5 NAG sing 275 n n C5 H5 NAG sing 276 n n C6 O6 NAG sing 277 n n C6 H61 NAG sing 278 n n C6 H62 NAG sing 279 n n C7 C8 NAG sing 280 n n C7 N2 NAG sing 281 n n C7 O7 NAG doub 282 n n C8 H81 NAG sing 283 n n C8 H82 NAG sing 284 n n C8 H83 NAG sing 285 n n N2 HN2 NAG sing 286 n n O1 HO1 NAG sing 287 n n O3 HO3 NAG sing 288 n n O4 HO4 NAG sing 289 n n O6 HO6 NAG sing 290 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 4KVN _atom_sites.fract_transf_matrix[1][1] 0.004893 _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] 0.004893 _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] 0.004893 _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 G 6 NAG A 1 604 9057 NAG NAG . H 6 NAG A 1 605 9120 NAG NAG . I 6 NAG A 1 606 9127 NAG NAG . J 6 NAG A 1 612 9279 NAG NAG . K 6 NAG A 1 613 9477 NAG NAG . L 7 PO4 L 1 301 2 PO4 PO4 . M 8 PGE L 1 302 1 PGE PGE . N 9 HOH A 1 701 1 HOH HOH . N 9 HOH A 2 702 2 HOH HOH . N 9 HOH A 3 703 4 HOH HOH . N 9 HOH A 4 704 5 HOH HOH . O 9 HOH L 1 401 3 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 . . . G 6 -0.158 32.858 -52.939 1 97.44 ? C1 NAG 604 A 1 HETATM 2 C C2 NAG . . . G 6 0.565 32.459 -51.65 1 98.87 ? C2 NAG 604 A 1 HETATM 3 C C3 NAG . . . G 6 1.71 33.417 -51.313 1 97.42 ? C3 NAG 604 A 1 HETATM 4 C C4 NAG . . . G 6 2.593 33.689 -52.533 1 95.88 ? C4 NAG 604 A 1 HETATM 5 C C5 NAG . . . G 6 1.754 34.057 -53.757 1 95.06 ? C5 NAG 604 A 1 HETATM 6 C C6 NAG . . . G 6 2.571 34.18 -55.024 1 95.02 ? C6 NAG 604 A 1 HETATM 7 C C7 NAG . . . G 6 -1.105 31.378 -50.176 1 102.06 ? C7 NAG 604 A 1 HETATM 8 C C8 NAG . . . G 6 -2.202 31.63 -49.186 1 101.81 ? C8 NAG 604 A 1 HETATM 9 N N2 NAG . . . G 6 -0.425 32.463 -50.583 1 100.86 ? N2 NAG 604 A 1 HETATM 10 O O3 NAG . . . G 6 2.497 32.85 -50.268 1 96.51 ? O3 NAG 604 A 1 HETATM 11 O O4 NAG . . . G 6 3.496 34.753 -52.234 1 95 ? O4 NAG 604 A 1 HETATM 12 O O5 NAG . . . G 6 0.779 33.032 -54.002 1 95.71 ? O5 NAG 604 A 1 HETATM 13 O O6 NAG . . . G 6 1.758 34.438 -56.163 1 94.57 ? O6 NAG 604 A 1 HETATM 14 O O7 NAG . . . G 6 -0.857 30.252 -50.6 1 103.19 ? O7 NAG 604 A 1 # _model_server_stats.io_time_ms 103 _model_server_stats.parse_time_ms 28 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 311 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 14 #