data_6QM3 # _model_server_result.job_id FWpK7xd4X5fkIqTQT1jH0Q _model_server_result.datetime_utc '2024-10-19 11:36:28' _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 6qm3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":503}' # _entry.id 6QM3 # _exptl.entry_id 6QM3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 8 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 117.435 _cell.angle_gamma 90 _cell.entry_id 6QM3 _cell.length_a 160.705 _cell.length_b 46.971 _cell.length_c 104.952 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6QM3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall 'C 2y' _symmetry.space_group_name_H-M 'C 1 2 1' # _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,M,N,O,P,Q,R,S,T _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 ? 2 C N N ? 2 D N N ? 2 E N N ? 2 F N N ? 2 L N N ? 2 M N N ? 2 N N N ? 2 O N 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 11 A CYS 221 1_555 B SG CYS 11 B CYS 221 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf2 A SG CYS 17 A CYS 227 1_555 A SG CYS 199 A CYS 409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf3 B SG CYS 17 B CYS 227 1_555 B SG CYS 199 B CYS 409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? covale ? covale1 A ND2 ASN 78 A ASN 288 1_555 C C1 NAG . A NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale2 A ND2 ASN 97 A ASN 307 1_555 D C1 NAG . A NAG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale3 A ND2 ASN 184 A ASN 394 1_555 E C1 NAG . A NAG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale4 A ND2 ASN 263 A ASN 473 1_555 F C1 NAG . A NAG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale5 B ND2 ASN 78 B ASN 288 1_555 L C1 NAG . B NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale6 B ND2 ASN 97 B ASN 307 1_555 M C1 NAG . B NAG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale7 B ND2 ASN 184 B ASN 394 1_555 N C1 NAG . B NAG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale8 B ND2 ASN 263 B ASN 473 1_555 O C1 NAG . B NAG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? metalc ? metalc1 A O GLY 92 A GLY 302 1_555 I NA NA . A NA 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.066 ? metalc ? metalc2 A OD2 ASP 146 A ASP 356 1_555 H CA CA . A CA 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.461 ? metalc ? metalc3 A OD1 ASP 146 A ASP 356 1_555 I NA NA . A NA 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.466 ? metalc ? metalc4 A O LEU 147 A LEU 357 1_555 I NA NA . A NA 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? metalc ? metalc5 A OE1 GLU 194 A GLU 404 1_555 H CA CA . A CA 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.372 ? metalc ? metalc6 A O ALA 195 A ALA 405 1_555 H CA CA . A CA 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.396 ? metalc ? metalc7 A O LEU 242 A LEU 452 1_555 H CA CA . A CA 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.363 ? metalc ? metalc8 A OD1 ASP 243 A ASP 453 1_555 H CA CA . A CA 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? metalc ? metalc9 A OD2 ASP 243 A ASP 453 1_555 I NA NA . A NA 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.346 ? metalc ? metalc10 H CA CA . A CA 506 1_555 S O HOH . A HOH 616 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.664 ? metalc ? metalc11 I NA NA . A NA 507 1_555 S O HOH . A HOH 619 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.319 ? metalc ? metalc12 B OD2 ASP 146 B ASP 356 1_555 P CA CA . B CA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.556 ? metalc ? metalc13 B OD1 ASP 146 B ASP 356 1_555 Q NA NA . B NA 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.706 ? metalc ? metalc14 B O LEU 147 B LEU 357 1_555 Q NA NA . B NA 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? metalc ? metalc15 B OE1 GLU 194 B GLU 404 1_555 P CA CA . B CA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.925 ? metalc ? metalc16 B O ALA 195 B ALA 405 1_555 P CA CA . B CA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.623 ? metalc ? metalc17 B O LEU 242 B LEU 452 1_555 P CA CA . B CA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.646 ? metalc ? metalc18 B OD1 ASP 243 B ASP 453 1_555 Q NA NA . B NA 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.066 ? metalc ? metalc19 B OD2 ASP 243 B ASP 453 1_555 Q NA NA . B NA 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.649 ? metalc ? metalc20 P CA CA . B CA 505 1_555 T O HOH . B HOH 645 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.315 ? metalc ? metalc21 Q NA NA . B NA 506 1_555 T O HOH . B HOH 621 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.667 ? # _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 253 n n C1 O1 NAG sing 254 n n C1 O5 NAG sing 255 n n C1 H1 NAG sing 256 n n C2 C3 NAG sing 257 n n C2 N2 NAG sing 258 n n C2 H2 NAG sing 259 n n C3 C4 NAG sing 260 n n C3 O3 NAG sing 261 n n C3 H3 NAG sing 262 n n C4 C5 NAG sing 263 n n C4 O4 NAG sing 264 n n C4 H4 NAG sing 265 n n C5 C6 NAG sing 266 n n C5 O5 NAG sing 267 n n C5 H5 NAG sing 268 n n C6 O6 NAG sing 269 n n C6 H61 NAG sing 270 n n C6 H62 NAG sing 271 n n C7 C8 NAG sing 272 n n C7 N2 NAG sing 273 n n C7 O7 NAG doub 274 n n C8 H81 NAG sing 275 n n C8 H82 NAG sing 276 n n C8 H83 NAG sing 277 n n N2 HN2 NAG sing 278 n n O1 HO1 NAG sing 279 n n O3 HO3 NAG sing 280 n n O4 HO4 NAG sing 281 n n O6 HO6 NAG sing 282 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 6QM3 _atom_sites.fract_transf_matrix[1][1] 0.006223 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00323 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.02129 _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] 0.010736 _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 C 2 NAG A 1 501 1288 NAG NAG . D 2 NAG A 1 502 1307 NAG NAG . E 2 NAG A 1 503 1394 NAG NAG . F 2 NAG A 1 504 1473 NAG NAG . G 3 CAC A 1 505 1 CAC CAC . H 4 CA A 1 506 1 CA CA . I 5 NA A 1 507 2 NA NA . J 6 ACT A 1 508 1 ACT ACT . K 6 ACT A 1 509 2 ACT ACT . L 2 NAG B 1 501 1288 NAG NAG . M 2 NAG B 1 502 1307 NAG NAG . N 2 NAG B 1 503 1394 NAG NAG . O 2 NAG B 1 504 1473 NAG NAG . P 4 CA B 1 505 3 CA CA . Q 5 NA B 1 506 4 NA NA . R 6 ACT B 1 507 3 ACT ACT . S 7 HOH A 1 601 62 HOH HOH . S 7 HOH A 2 602 69 HOH HOH . S 7 HOH A 3 603 85 HOH HOH . S 7 HOH A 4 604 65 HOH HOH . S 7 HOH A 5 605 52 HOH HOH . S 7 HOH A 6 606 15 HOH HOH . S 7 HOH A 7 607 1 HOH HOH . S 7 HOH A 8 608 68 HOH HOH . S 7 HOH A 9 609 17 HOH HOH . S 7 HOH A 10 610 13 HOH HOH . S 7 HOH A 11 611 4 HOH HOH . S 7 HOH A 12 612 53 HOH HOH . S 7 HOH A 13 613 21 HOH HOH . S 7 HOH A 14 614 34 HOH HOH . S 7 HOH A 15 615 22 HOH HOH . S 7 HOH A 16 616 48 HOH HOH . S 7 HOH A 17 617 8 HOH HOH . S 7 HOH A 18 618 49 HOH HOH . S 7 HOH A 19 619 25 HOH HOH . S 7 HOH A 20 620 36 HOH HOH . S 7 HOH A 21 621 24 HOH HOH . S 7 HOH A 22 622 47 HOH HOH . S 7 HOH A 23 623 16 HOH HOH . S 7 HOH A 24 624 61 HOH HOH . S 7 HOH A 25 625 63 HOH HOH . S 7 HOH A 26 626 19 HOH HOH . S 7 HOH A 27 627 2 HOH HOH . S 7 HOH A 28 628 58 HOH HOH . S 7 HOH A 29 629 33 HOH HOH . S 7 HOH A 30 630 97 HOH HOH . S 7 HOH A 31 631 51 HOH HOH . S 7 HOH A 32 632 5 HOH HOH . S 7 HOH A 33 633 83 HOH HOH . S 7 HOH A 34 634 41 HOH HOH . S 7 HOH A 35 635 89 HOH HOH . S 7 HOH A 36 636 81 HOH HOH . S 7 HOH A 37 637 35 HOH HOH . S 7 HOH A 38 638 44 HOH HOH . S 7 HOH A 39 639 79 HOH HOH . S 7 HOH A 40 640 56 HOH HOH . S 7 HOH A 41 641 45 HOH HOH . S 7 HOH A 42 642 46 HOH HOH . S 7 HOH A 43 643 98 HOH HOH . S 7 HOH A 44 644 95 HOH HOH . S 7 HOH A 45 645 82 HOH HOH . S 7 HOH A 46 646 28 HOH HOH . S 7 HOH A 47 647 84 HOH HOH . T 7 HOH B 1 601 80 HOH HOH . T 7 HOH B 2 602 30 HOH HOH . T 7 HOH B 3 603 23 HOH HOH . T 7 HOH B 4 604 39 HOH HOH . T 7 HOH B 5 605 74 HOH HOH . T 7 HOH B 6 606 31 HOH HOH . T 7 HOH B 7 607 99 HOH HOH . T 7 HOH B 8 608 59 HOH HOH . T 7 HOH B 9 609 27 HOH HOH . T 7 HOH B 10 610 67 HOH HOH . T 7 HOH B 11 611 96 HOH HOH . T 7 HOH B 12 612 75 HOH HOH . T 7 HOH B 13 613 54 HOH HOH . T 7 HOH B 14 614 77 HOH HOH . T 7 HOH B 15 615 10 HOH HOH . T 7 HOH B 16 616 3 HOH HOH . T 7 HOH B 17 617 76 HOH HOH . T 7 HOH B 18 618 50 HOH HOH . T 7 HOH B 19 619 11 HOH HOH . T 7 HOH B 20 620 32 HOH HOH . T 7 HOH B 21 621 73 HOH HOH . T 7 HOH B 22 622 42 HOH HOH . T 7 HOH B 23 623 94 HOH HOH . T 7 HOH B 24 624 55 HOH HOH . T 7 HOH B 25 625 9 HOH HOH . T 7 HOH B 26 626 26 HOH HOH . T 7 HOH B 27 627 20 HOH HOH . T 7 HOH B 28 628 57 HOH HOH . T 7 HOH B 29 629 7 HOH HOH . T 7 HOH B 30 630 60 HOH HOH . T 7 HOH B 31 631 29 HOH HOH . T 7 HOH B 32 632 88 HOH HOH . T 7 HOH B 33 633 91 HOH HOH . T 7 HOH B 34 634 12 HOH HOH . T 7 HOH B 35 635 14 HOH HOH . T 7 HOH B 36 636 43 HOH HOH . T 7 HOH B 37 637 70 HOH HOH . T 7 HOH B 38 638 18 HOH HOH . T 7 HOH B 39 639 6 HOH HOH . T 7 HOH B 40 640 66 HOH HOH . T 7 HOH B 41 641 40 HOH HOH . T 7 HOH B 42 642 93 HOH HOH . T 7 HOH B 43 643 86 HOH HOH . T 7 HOH B 44 644 37 HOH HOH . T 7 HOH B 45 645 87 HOH HOH . T 7 HOH B 46 646 64 HOH HOH . T 7 HOH B 47 647 38 HOH HOH . T 7 HOH B 48 648 90 HOH HOH . T 7 HOH B 49 649 92 HOH HOH . T 7 HOH B 50 650 78 HOH HOH . T 7 HOH B 51 651 72 HOH HOH . T 7 HOH B 52 652 71 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 . . . N 2 82.784 4.275 51.177 1 55.59 ? C1 NAG 503 B 1 HETATM 2 C C2 NAG . . . N 2 81.838 3.196 51.722 1 65.32 ? C2 NAG 503 B 1 HETATM 3 C C3 NAG . . . N 2 82.639 1.998 52.235 1 76.7 ? C3 NAG 503 B 1 HETATM 4 C C4 NAG . . . N 2 83.574 1.476 51.152 1 77.62 ? C4 NAG 503 B 1 HETATM 5 C C5 NAG . . . N 2 84.469 2.604 50.649 1 77.05 ? C5 NAG 503 B 1 HETATM 6 C C6 NAG . . . N 2 85.362 2.181 49.504 1 80.9 ? C6 NAG 503 B 1 HETATM 7 C C7 NAG . . . N 2 79.718 4.108 52.562 1 50.02 ? C7 NAG 503 B 1 HETATM 8 C C8 NAG . . . N 2 78.971 4.597 53.767 1 44.16 ? C8 NAG 503 B 1 HETATM 9 N N2 NAG . . . N 2 80.978 3.716 52.774 1 57.74 ? N2 NAG 503 B 1 HETATM 10 O O3 NAG . . . N 2 81.753 0.964 52.649 1 83.45 ? O3 NAG 503 B 1 HETATM 11 O O4 NAG . . . N 2 84.387 0.429 51.671 1 75.96 ? O4 NAG 503 B 1 HETATM 12 O O5 NAG . . . N 2 83.66 3.694 50.176 1 68.42 ? O5 NAG 503 B 1 HETATM 13 O O6 NAG . . . N 2 85.159 2.973 48.342 1 85.48 ? O6 NAG 503 B 1 HETATM 14 O O7 NAG . . . N 2 79.206 4.078 51.443 1 53.3 ? O7 NAG 503 B 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 303 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 14 #