data_9AVL # _model_server_result.job_id 9hN1fzwTuR5bOgC9rJ2ZDw _model_server_result.datetime_utc '2024-12-26 12:55:04' _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 9avl # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"R","auth_seq_id":1001}' # _entry.id 9AVL # _exptl.entry_id 9AVL _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 221.208 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _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 9AVL _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 9AVL _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details pentameric _pdbx_struct_assembly.oligomeric_count 5 _pdbx_struct_assembly.details author_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,U,V,W,X,Y,Z,AA _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 ? _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 ? 6 J N N ? 6 R N N ? 6 S N N ? 6 T N N # _pdbx_entity_branch.entity_id 5 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 5 _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 5 n F NAG 1 C 1 NAG C 1 NAG 5 n F NAG 2 C 2 NAG C 2 NAG 5 n G NAG 1 D 1 NAG D 1 NAG 5 n G NAG 2 D 2 NAG D 2 NAG 5 n H NAG 1 E 1 NAG E 1 NAG 5 n H NAG 2 E 2 NAG E 2 NAG 5 n I NAG 1 F 1 NAG F 1 NAG 5 n I NAG 2 F 2 NAG F 2 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 68 Q CYS 60 1_555 A SG CYS 109 Q CYS 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf2 A SG CYS 244 Q CYS 236 1_555 A SG CYS 569 Q CYS 561 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf3 A SG CYS 366 Q CYS 358 1_555 A SG CYS 403 Q CYS 395 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf4 A SG CYS 550 Q CYS 542 1_555 A SG CYS 570 Q CYS 562 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf5 A SG CYS 554 Q CYS 546 1_555 A SG CYS 573 Q CYS 565 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf6 A SG CYS 576 Q CYS 568 1_555 A SG CYS 590 Q CYS 582 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf7 A SG CYS 593 Q CYS 585 1_555 A SG CYS 606 Q CYS 598 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf8 A SG CYS 685 Q CYS 677 1_555 A SG CYS 773 Q CYS 765 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf9 B SG CYS 68 R CYS 60 1_555 B SG CYS 109 R CYS 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf10 B SG CYS 244 R CYS 236 1_555 B SG CYS 569 R CYS 561 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf11 B SG CYS 366 R CYS 358 1_555 B SG CYS 403 R CYS 395 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf12 B SG CYS 445 R CYS 437 1_555 B SG CYS 457 R CYS 449 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf13 B SG CYS 550 R CYS 542 1_555 B SG CYS 570 R CYS 562 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf14 B SG CYS 554 R CYS 546 1_555 B SG CYS 573 R CYS 565 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf15 B SG CYS 576 R CYS 568 1_555 B SG CYS 590 R CYS 582 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf16 B SG CYS 593 R CYS 585 1_555 B SG CYS 606 R CYS 598 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf17 B SG CYS 685 R CYS 677 1_555 B SG CYS 773 R CYS 765 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? covale ? covale1 A ND2 ASN 476 Q ASN 468 1_555 J C1 NAG . Q NAG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale2 A ND2 ASN 496 Q ASN 488 1_555 F C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale3 A ND2 ASN 549 Q ASN 541 1_555 G C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale4 B ND2 ASN 269 R ASN 261 1_555 R C1 NAG . R NAG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale5 B ND2 ASN 295 R ASN 287 1_555 S C1 NAG . R NAG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale6 B ND2 ASN 476 R ASN 468 1_555 T C1 NAG . R NAG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale7 B ND2 ASN 496 R ASN 488 1_555 H C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale8 B ND2 ASN 549 R ASN 541 1_555 I C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale9 F O4 NAG . C NAG 1 1_555 F C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale10 G O4 NAG . D NAG 1 1_555 G C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale11 H O4 NAG . E NAG 1 1_555 H C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale12 I O4 NAG . F NAG 1 1_555 I C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? metalc ? metalc1 A OG1 THR 108 Q THR 100 1_555 M CA CA . Q CA 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.461 ? metalc ? metalc2 A O GLY 565 Q GLY 557 1_555 O CA CA . Q CA 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.499 ? metalc ? metalc3 B O GLY 565 R GLY 557 1_555 Y CA CA . R CA 1008 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.499 ? # _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 406 n n C1 O1 NAG sing 407 n n C1 O5 NAG sing 408 n n C1 H1 NAG sing 409 n n C2 C3 NAG sing 410 n n C2 N2 NAG sing 411 n n C2 H2 NAG sing 412 n n C3 C4 NAG sing 413 n n C3 O3 NAG sing 414 n n C3 H3 NAG sing 415 n n C4 C5 NAG sing 416 n n C4 O4 NAG sing 417 n n C4 H4 NAG sing 418 n n C5 C6 NAG sing 419 n n C5 O5 NAG sing 420 n n C5 H5 NAG sing 421 n n C6 O6 NAG sing 422 n n C6 H61 NAG sing 423 n n C6 H62 NAG sing 424 n n C7 C8 NAG sing 425 n n C7 N2 NAG sing 426 n n C7 O7 NAG doub 427 n n C8 H81 NAG sing 428 n n C8 H82 NAG sing 429 n n C8 H83 NAG sing 430 n n N2 HN2 NAG sing 431 n n O1 HO1 NAG sing 432 n n O3 HO3 NAG sing 433 n n O4 HO4 NAG sing 434 n n O6 HO6 NAG sing 435 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 9AVL _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 J 6 NAG Q 1 1001 1004 NAG NAG . K 7 TCR Q 1 1002 1 TCR TCR . L 8 PO4 Q 1 1003 2 PO4 PO4 . M 9 CA Q 1 1004 4 CA CA . N 9 CA Q 1 1005 6 CA CA . O 9 CA Q 1 1006 7 CA CA . P 10 9IG Q 1 1007 1 9IG 568 . Q 11 Y01 Q 1 1008 1 Y01 Y01 . R 6 NAG R 1 1001 1002 NAG NAG . S 6 NAG R 1 1002 1003 NAG NAG . T 6 NAG R 1 1003 1004 NAG NAG . U 7 TCR R 1 1004 1 TCR TCR . V 8 PO4 R 1 1005 1 PO4 PO4 . W 9 CA R 1 1006 3 CA CA . X 9 CA R 1 1007 5 CA CA . Y 9 CA R 1 1008 8 CA CA . Z 10 9IG R 1 1009 1 9IG 568 . AA 12 A1AF7 R 1 1010 1 A1AF7 PG1 . # 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 . . . R 6 213.878 230.042 295.812 1 58.7 ? C1 NAG 1001 R 1 HETATM 2 C C2 NAG . . . R 6 215.016 229.387 296.592 1 58.7 ? C2 NAG 1001 R 1 HETATM 3 C C3 NAG . . . R 6 215.93 230.454 297.186 1 58.7 ? C3 NAG 1001 R 1 HETATM 4 C C4 NAG . . . R 6 216.408 231.409 296.101 1 58.7 ? C4 NAG 1001 R 1 HETATM 5 C C5 NAG . . . R 6 215.217 231.978 295.335 1 58.7 ? C5 NAG 1001 R 1 HETATM 6 C C6 NAG . . . R 6 215.626 232.836 294.16 1 58.7 ? C6 NAG 1001 R 1 HETATM 7 C C7 NAG . . . R 6 214.882 227.245 297.782 1 58.7 ? C7 NAG 1001 R 1 HETATM 8 C C8 NAG . . . R 6 214.254 226.497 298.917 1 58.7 ? C8 NAG 1001 R 1 HETATM 9 N N2 NAG . . . R 6 214.5 228.518 297.637 1 58.7 ? N2 NAG 1001 R 1 HETATM 10 O O3 NAG . . . R 6 217.044 229.828 297.811 1 58.7 ? O3 NAG 1001 R 1 HETATM 11 O O4 NAG . . . R 6 217.145 232.478 296.684 1 58.7 ? O4 NAG 1001 R 1 HETATM 12 O O5 NAG . . . R 6 214.42 230.908 294.807 1 58.7 ? O5 NAG 1001 R 1 HETATM 13 O O6 NAG . . . R 6 216.589 232.178 293.349 1 58.7 ? O6 NAG 1001 R 1 HETATM 14 O O7 NAG . . . R 6 215.699 226.722 297.031 1 58.7 ? O7 NAG 1001 R 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 64 _model_server_stats.query_time_ms 340 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 14 #