data_3VCM # _model_server_result.job_id U690m1ZxITts1EH9_YHTRw _model_server_result.datetime_utc '2025-03-09 02:04:38' _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 3vcm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":401}' # _entry.id 3VCM # _exptl.entry_id 3VCM _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 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 90 _cell.entry_id 3VCM _cell.length_a 104.42 _cell.length_b 104.42 _cell.length_c 237.12 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3VCM _symmetry.cell_setting ? _symmetry.Int_Tables_number 95 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 2 2' # 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 dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 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,C,E,F,H 1 1 B,D,G,I 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 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id E _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # 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 51 A CYS 45 1_555 A SG CYS 58 A CYS 50 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf2 A SG CYS 212 A CYS 206 1_555 A SG CYS 216 A CYS 210 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf3 A SG CYS 254 A CYS 249 1_555 A SG CYS 291 A CYS 282 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf4 B SG CYS 51 B CYS 45 1_555 B SG CYS 58 B CYS 50 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf5 B SG CYS 212 B CYS 206 1_555 B SG CYS 216 B CYS 210 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf6 B SG CYS 254 B CYS 249 1_555 B SG CYS 291 B CYS 282 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? covale ? covale1 A ND2 ASN 75 A ASN 67 1_555 E C1 NAG . A NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.474 ? # _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 237 n n C1 O1 NAG sing 238 n n C1 O5 NAG sing 239 n n C1 H1 NAG sing 240 n n C2 C3 NAG sing 241 n n C2 N2 NAG sing 242 n n C2 H2 NAG sing 243 n n C3 C4 NAG sing 244 n n C3 O3 NAG sing 245 n n C3 H3 NAG sing 246 n n C4 C5 NAG sing 247 n n C4 O4 NAG sing 248 n n C4 H4 NAG sing 249 n n C5 C6 NAG sing 250 n n C5 O5 NAG sing 251 n n C5 H5 NAG sing 252 n n C6 O6 NAG sing 253 n n C6 H61 NAG sing 254 n n C6 H62 NAG sing 255 n n C7 C8 NAG sing 256 n n C7 N2 NAG sing 257 n n C7 O7 NAG doub 258 n n C8 H81 NAG sing 259 n n C8 H82 NAG sing 260 n n C8 H83 NAG sing 261 n n N2 HN2 NAG sing 262 n n O1 HO1 NAG sing 263 n n O3 HO3 NAG sing 264 n n O4 HO4 NAG sing 265 n n O6 HO6 NAG sing 266 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 3VCM _atom_sites.fract_transf_matrix[1][1] 0.009577 _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] 0.009577 _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] 0.004217 _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 1 401 390 NAG NAG . F 4 HOH A 1 501 3 HOH HOH . F 4 HOH A 2 502 6 HOH HOH . F 4 HOH A 3 503 7 HOH HOH . F 4 HOH A 4 504 9 HOH HOH . F 4 HOH A 5 505 13 HOH HOH . F 4 HOH A 6 506 20 HOH HOH . F 4 HOH A 7 507 22 HOH HOH . F 4 HOH A 8 508 23 HOH HOH . F 4 HOH A 9 509 27 HOH HOH . F 4 HOH A 10 510 29 HOH HOH . F 4 HOH A 11 511 30 HOH HOH . F 4 HOH A 12 512 35 HOH HOH . F 4 HOH A 13 513 41 HOH HOH . F 4 HOH A 14 514 44 HOH HOH . F 4 HOH A 15 515 61 HOH HOH . F 4 HOH A 16 516 62 HOH HOH . F 4 HOH A 17 517 72 HOH HOH . F 4 HOH A 18 518 81 HOH HOH . F 4 HOH A 19 519 98 HOH HOH . F 4 HOH A 20 520 100 HOH HOH . F 4 HOH A 21 521 104 HOH HOH . F 4 HOH A 22 522 140 HOH HOH . F 4 HOH A 23 523 151 HOH HOH . F 4 HOH A 24 524 153 HOH HOH . F 4 HOH A 25 525 156 HOH HOH . F 4 HOH A 26 526 158 HOH HOH . F 4 HOH A 27 527 189 HOH HOH . F 4 HOH A 28 528 190 HOH HOH . F 4 HOH A 29 529 206 HOH HOH . F 4 HOH A 30 530 221 HOH HOH . F 4 HOH A 31 531 225 HOH HOH . F 4 HOH A 32 532 229 HOH HOH . F 4 HOH A 33 533 232 HOH HOH . F 4 HOH A 34 534 234 HOH HOH . F 4 HOH A 35 535 257 HOH HOH . F 4 HOH A 36 536 267 HOH HOH . G 4 HOH B 1 401 2 HOH HOH . G 4 HOH B 2 402 12 HOH HOH . G 4 HOH B 3 403 14 HOH HOH . G 4 HOH B 4 404 15 HOH HOH . G 4 HOH B 5 405 17 HOH HOH . G 4 HOH B 6 406 18 HOH HOH . G 4 HOH B 7 407 19 HOH HOH . G 4 HOH B 8 408 21 HOH HOH . G 4 HOH B 9 409 24 HOH HOH . G 4 HOH B 10 410 32 HOH HOH . G 4 HOH B 11 411 33 HOH HOH . G 4 HOH B 12 412 34 HOH HOH . G 4 HOH B 13 413 38 HOH HOH . G 4 HOH B 14 414 39 HOH HOH . G 4 HOH B 15 415 45 HOH HOH . G 4 HOH B 16 416 46 HOH HOH . G 4 HOH B 17 417 50 HOH HOH . G 4 HOH B 18 418 52 HOH HOH . G 4 HOH B 19 419 55 HOH HOH . G 4 HOH B 20 420 64 HOH HOH . G 4 HOH B 21 421 66 HOH HOH . G 4 HOH B 22 422 77 HOH HOH . G 4 HOH B 23 423 87 HOH HOH . G 4 HOH B 24 424 94 HOH HOH . G 4 HOH B 25 425 96 HOH HOH . G 4 HOH B 26 426 97 HOH HOH . G 4 HOH B 27 427 102 HOH HOH . G 4 HOH B 28 428 103 HOH HOH . G 4 HOH B 29 429 123 HOH HOH . G 4 HOH B 30 430 137 HOH HOH . G 4 HOH B 31 431 138 HOH HOH . G 4 HOH B 32 432 142 HOH HOH . G 4 HOH B 33 433 143 HOH HOH . G 4 HOH B 34 434 146 HOH HOH . G 4 HOH B 35 435 150 HOH HOH . G 4 HOH B 36 436 154 HOH HOH . G 4 HOH B 37 437 166 HOH HOH . G 4 HOH B 38 438 175 HOH HOH . G 4 HOH B 39 439 182 HOH HOH . G 4 HOH B 40 440 188 HOH HOH . G 4 HOH B 41 441 197 HOH HOH . G 4 HOH B 42 442 211 HOH HOH . G 4 HOH B 43 443 213 HOH HOH . G 4 HOH B 44 444 214 HOH HOH . G 4 HOH B 45 445 247 HOH HOH . G 4 HOH B 46 446 251 HOH HOH . G 4 HOH B 47 447 252 HOH HOH . G 4 HOH B 48 448 264 HOH HOH . G 4 HOH B 49 449 265 HOH HOH . H 4 HOH P 1 101 4 HOH HOH . H 4 HOH P 2 102 36 HOH HOH . H 4 HOH P 3 103 48 HOH HOH . H 4 HOH P 4 104 51 HOH HOH . H 4 HOH P 5 105 69 HOH HOH . H 4 HOH P 6 106 75 HOH HOH . H 4 HOH P 7 107 107 HOH HOH . H 4 HOH P 8 108 124 HOH HOH . I 4 HOH Q 1 101 163 HOH HOH . I 4 HOH Q 2 102 168 HOH HOH . I 4 HOH Q 3 103 196 HOH HOH . I 4 HOH Q 4 104 223 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 . . . E 3 -64.296 -8.101 25.014 1 50.75 ? C1 NAG 401 A 1 HETATM 2 C C2 NAG . . . E 3 -65.826 -8.217 25.269 1 53.2 ? C2 NAG 401 A 1 HETATM 3 C C3 NAG . . . E 3 -66.492 -6.825 25.035 1 55.19 ? C3 NAG 401 A 1 HETATM 4 C C4 NAG . . . E 3 -65.807 -5.691 25.87 1 55.82 ? C4 NAG 401 A 1 HETATM 5 C C5 NAG . . . E 3 -64.267 -5.751 25.742 1 54.26 ? C5 NAG 401 A 1 HETATM 6 C C6 NAG . . . E 3 -63.588 -4.837 26.78 1 55.72 ? C6 NAG 401 A 1 HETATM 7 C C7 NAG . . . E 3 -66.611 -10.6 24.947 1 55.8 ? C7 NAG 401 A 1 HETATM 8 C C8 NAG . . . E 3 -67.293 -11.497 23.946 1 56.5 ? C8 NAG 401 A 1 HETATM 9 N N2 NAG . . . E 3 -66.458 -9.302 24.503 1 54.39 ? N2 NAG 401 A 1 HETATM 10 O O3 NAG . . . E 3 -67.906 -6.911 25.328 1 58.37 ? O3 NAG 401 A 1 HETATM 11 O O4 NAG . . . E 3 -66.252 -4.386 25.454 1 59.03 ? O4 NAG 401 A 1 HETATM 12 O O5 NAG . . . E 3 -63.774 -7.108 25.928 1 52.2 ? O5 NAG 401 A 1 HETATM 13 O O6 NAG . . . E 3 -62.327 -4.359 26.3 1 57.23 ? O6 NAG 401 A 1 HETATM 14 O O7 NAG . . . E 3 -66.238 -11.016 26.053 1 57.66 ? O7 NAG 401 A 1 # _model_server_stats.io_time_ms 198 _model_server_stats.parse_time_ms 95 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 289 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 14 #