data_1DLH # _model_server_result.job_id -dLqOxXmcAidZJKhp7wp1w _model_server_result.datetime_utc '2024-11-15 10:46:57' _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 1dlh # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":521}' # _entry.id 1DLH # _exptl.entry_id 1DLH _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 5 _entity.src_method man _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 1DLH _cell.length_a 94.6 _cell.length_b 94.6 _cell.length_c 247.5 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1DLH _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 43 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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 _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 ? 5 I N N ? 5 J N N ? 5 K N N ? 5 L N N # _pdbx_entity_branch.entity_id 4 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 4 _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 NDG _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 4 n G NAG 1 G 1 NAG B 511 NAG 4 n G NDG 2 G 2 NDG B 512 NAG 4 n H NAG 1 H 1 NAG E 511 NAG 4 n H NDG 2 H 2 NDG E 512 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 105 A CYS 107 1_555 A SG CYS 161 A CYS 163 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.007 ? disulf ? disulf2 B SG CYS 13 B CYS 15 1_555 B SG CYS 77 B CYS 79 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? disulf ? disulf3 B SG CYS 115 B CYS 117 1_555 B SG CYS 171 B CYS 173 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf4 D SG CYS 105 D CYS 107 1_555 D SG CYS 161 D CYS 163 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf5 E SG CYS 13 E CYS 15 1_555 E SG CYS 77 E CYS 79 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? disulf ? disulf6 E SG CYS 115 E CYS 117 1_555 E SG CYS 171 E CYS 173 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? covale ? covale1 A ND2 ASN 76 A ASN 78 1_555 I C1 NAG . A NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale2 A ND2 ASN 116 A ASN 118 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.478 ? covale ? covale3 B ND2 ASN 17 B ASN 19 1_555 J C1 NAG . B NAG 521 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale4 D ND2 ASN 76 D ASN 78 1_555 K C1 NAG . D NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.474 ? covale ? covale5 D ND2 ASN 116 D ASN 118 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.459 ? covale ? covale6 E ND2 ASN 17 E ASN 19 1_555 L C1 NAG . E NAG 521 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.488 ? covale ? covale7 G O4 NAG . G NAG 1 1_555 G C1 NDG . G NDG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.401 ? covale ? covale8 H O4 NAG . H NAG 1 1_555 H C1 NDG . H NDG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.407 ? # _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 1DLH _atom_sites.fract_transf_matrix[1][1] 0.010571 _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] 0.010571 _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] 0.00404 _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 I 5 NAG A 1 501 501 NAG NAG . J 5 NAG B 1 521 521 NAG NAG . K 5 NAG D 1 501 501 NAG NAG . L 5 NAG E 1 521 521 NAG NAG . M 6 HOH A 1 502 3 HOH HOH . M 6 HOH A 2 503 14 HOH HOH . M 6 HOH A 3 504 16 HOH HOH . M 6 HOH A 4 505 22 HOH HOH . M 6 HOH A 5 506 39 HOH HOH . M 6 HOH A 6 507 47 HOH HOH . M 6 HOH A 7 508 54 HOH HOH . M 6 HOH A 8 509 55 HOH HOH . M 6 HOH A 9 510 62 HOH HOH . M 6 HOH A 10 511 66 HOH HOH . M 6 HOH A 11 512 68 HOH HOH . M 6 HOH A 12 513 69 HOH HOH . M 6 HOH A 13 514 70 HOH HOH . M 6 HOH A 14 515 76 HOH HOH . M 6 HOH A 15 516 83 HOH HOH . M 6 HOH A 16 517 88 HOH HOH . M 6 HOH A 17 518 95 HOH HOH . M 6 HOH A 18 519 97 HOH HOH . M 6 HOH A 19 520 99 HOH HOH . M 6 HOH A 20 521 104 HOH HOH . M 6 HOH A 21 522 108 HOH HOH . M 6 HOH A 22 523 115 HOH HOH . M 6 HOH A 23 524 118 HOH HOH . M 6 HOH A 24 525 120 HOH HOH . M 6 HOH A 25 526 122 HOH HOH . M 6 HOH A 26 527 123 HOH HOH . M 6 HOH A 27 528 127 HOH HOH . M 6 HOH A 28 529 130 HOH HOH . M 6 HOH A 29 530 139 HOH HOH . M 6 HOH A 30 531 144 HOH HOH . M 6 HOH A 31 532 149 HOH HOH . M 6 HOH A 32 533 158 HOH HOH . M 6 HOH A 33 534 161 HOH HOH . M 6 HOH A 34 535 162 HOH HOH . M 6 HOH A 35 536 164 HOH HOH . M 6 HOH A 36 537 166 HOH HOH . M 6 HOH A 37 538 171 HOH HOH . M 6 HOH A 38 539 173 HOH HOH . N 6 HOH B 1 522 1 HOH HOH . N 6 HOH B 2 523 4 HOH HOH . N 6 HOH B 3 524 9 HOH HOH . N 6 HOH B 4 525 12 HOH HOH . N 6 HOH B 5 526 13 HOH HOH . N 6 HOH B 6 527 19 HOH HOH . N 6 HOH B 7 528 21 HOH HOH . N 6 HOH B 8 529 24 HOH HOH . N 6 HOH B 9 530 27 HOH HOH . N 6 HOH B 10 531 29 HOH HOH . N 6 HOH B 11 532 37 HOH HOH . N 6 HOH B 12 533 38 HOH HOH . N 6 HOH B 13 534 42 HOH HOH . N 6 HOH B 14 535 53 HOH HOH . N 6 HOH B 15 536 58 HOH HOH . N 6 HOH B 16 537 64 HOH HOH . N 6 HOH B 17 538 75 HOH HOH . N 6 HOH B 18 539 80 HOH HOH . N 6 HOH B 19 540 84 HOH HOH . N 6 HOH B 20 541 87 HOH HOH . N 6 HOH B 21 542 101 HOH HOH . N 6 HOH B 22 543 110 HOH HOH . N 6 HOH B 23 544 113 HOH HOH . N 6 HOH B 24 545 114 HOH HOH . N 6 HOH B 25 546 125 HOH HOH . N 6 HOH B 26 547 126 HOH HOH . N 6 HOH B 27 548 129 HOH HOH . N 6 HOH B 28 549 131 HOH HOH . N 6 HOH B 29 550 138 HOH HOH . N 6 HOH B 30 551 140 HOH HOH . N 6 HOH B 31 552 142 HOH HOH . N 6 HOH B 32 553 145 HOH HOH . N 6 HOH B 33 554 147 HOH HOH . N 6 HOH B 34 555 152 HOH HOH . N 6 HOH B 35 556 154 HOH HOH . N 6 HOH B 36 557 155 HOH HOH . N 6 HOH B 37 558 157 HOH HOH . N 6 HOH B 38 559 172 HOH HOH . N 6 HOH B 39 560 174 HOH HOH . N 6 HOH B 40 561 177 HOH HOH . O 6 HOH C 1 25 25 HOH HOH . O 6 HOH C 2 43 43 HOH HOH . P 6 HOH D 1 502 7 HOH HOH . P 6 HOH D 2 503 31 HOH HOH . P 6 HOH D 3 504 32 HOH HOH . P 6 HOH D 4 505 33 HOH HOH . P 6 HOH D 5 506 35 HOH HOH . P 6 HOH D 6 507 40 HOH HOH . P 6 HOH D 7 508 41 HOH HOH . P 6 HOH D 8 509 46 HOH HOH . P 6 HOH D 9 510 50 HOH HOH . P 6 HOH D 10 511 56 HOH HOH . P 6 HOH D 11 512 60 HOH HOH . P 6 HOH D 12 513 65 HOH HOH . P 6 HOH D 13 514 79 HOH HOH . P 6 HOH D 14 515 81 HOH HOH . P 6 HOH D 15 516 85 HOH HOH . P 6 HOH D 16 517 89 HOH HOH . P 6 HOH D 17 518 90 HOH HOH . P 6 HOH D 18 519 92 HOH HOH . P 6 HOH D 19 520 93 HOH HOH . P 6 HOH D 20 521 98 HOH HOH . P 6 HOH D 21 522 100 HOH HOH . P 6 HOH D 22 523 102 HOH HOH . P 6 HOH D 23 524 105 HOH HOH . P 6 HOH D 24 525 106 HOH HOH . P 6 HOH D 25 526 119 HOH HOH . P 6 HOH D 26 527 124 HOH HOH . P 6 HOH D 27 528 132 HOH HOH . P 6 HOH D 28 529 134 HOH HOH . P 6 HOH D 29 530 151 HOH HOH . P 6 HOH D 30 531 153 HOH HOH . P 6 HOH D 31 532 160 HOH HOH . P 6 HOH D 32 533 168 HOH HOH . P 6 HOH D 33 534 176 HOH HOH . P 6 HOH D 34 535 165 HOH HOH . Q 6 HOH E 1 522 2 HOH HOH . Q 6 HOH E 2 523 6 HOH HOH . Q 6 HOH E 3 524 10 HOH HOH . Q 6 HOH E 4 525 11 HOH HOH . Q 6 HOH E 5 526 17 HOH HOH . Q 6 HOH E 6 527 18 HOH HOH . Q 6 HOH E 7 528 20 HOH HOH . Q 6 HOH E 8 529 28 HOH HOH . Q 6 HOH E 9 530 34 HOH HOH . Q 6 HOH E 10 531 36 HOH HOH . Q 6 HOH E 11 532 48 HOH HOH . Q 6 HOH E 12 533 51 HOH HOH . Q 6 HOH E 13 534 52 HOH HOH . Q 6 HOH E 14 535 57 HOH HOH . Q 6 HOH E 15 536 59 HOH HOH . Q 6 HOH E 16 537 61 HOH HOH . Q 6 HOH E 17 538 71 HOH HOH . Q 6 HOH E 18 539 72 HOH HOH . Q 6 HOH E 19 540 74 HOH HOH . Q 6 HOH E 20 541 78 HOH HOH . Q 6 HOH E 21 542 86 HOH HOH . Q 6 HOH E 22 543 91 HOH HOH . Q 6 HOH E 23 544 107 HOH HOH . Q 6 HOH E 24 545 109 HOH HOH . Q 6 HOH E 25 546 112 HOH HOH . Q 6 HOH E 26 547 116 HOH HOH . Q 6 HOH E 27 548 121 HOH HOH . Q 6 HOH E 28 549 128 HOH HOH . Q 6 HOH E 29 550 135 HOH HOH . Q 6 HOH E 30 551 137 HOH HOH . Q 6 HOH E 31 552 143 HOH HOH . Q 6 HOH E 32 553 148 HOH HOH . Q 6 HOH E 33 554 159 HOH HOH . Q 6 HOH E 34 555 167 HOH HOH . Q 6 HOH E 35 556 169 HOH HOH . Q 6 HOH E 36 557 170 HOH HOH . R 6 HOH F 1 94 94 HOH HOH . R 6 HOH F 2 133 133 HOH HOH . R 6 HOH F 3 136 136 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 . . . L 5 -15.952 34.698 38.814 1 78.78 ? C1 NAG 521 E 1 HETATM 2 C C2 NAG . . . L 5 -16.731 34.777 40.169 1 79.8 ? C2 NAG 521 E 1 HETATM 3 C C3 NAG . . . L 5 -17.358 33.425 40.539 1 80.49 ? C3 NAG 521 E 1 HETATM 4 C C4 NAG . . . L 5 -17.326 32.463 39.38 1 80.65 ? C4 NAG 521 E 1 HETATM 5 C C5 NAG . . . L 5 -15.881 32.205 38.98 1 79.82 ? C5 NAG 521 E 1 HETATM 6 C C6 NAG . . . L 5 -15.699 31.305 37.766 1 78.36 ? C6 NAG 521 E 1 HETATM 7 C C7 NAG . . . L 5 -15.552 36.452 41.509 1 80.74 ? C7 NAG 521 E 1 HETATM 8 C C8 NAG . . . L 5 -14.589 36.711 42.654 1 80.17 ? C8 NAG 521 E 1 HETATM 9 N N2 NAG . . . L 5 -15.827 35.177 41.248 1 82.27 ? N2 NAG 521 E 1 HETATM 10 O O3 NAG . . . L 5 -18.697 33.594 40.968 1 83.44 ? O3 NAG 521 E 1 HETATM 11 O O4 NAG . . . L 5 -17.952 31.247 39.756 1 82.42 ? O4 NAG 521 E 1 HETATM 12 O O5 NAG . . . L 5 -15.154 33.457 38.751 1 82.01 ? O5 NAG 521 E 1 HETATM 13 O O6 NAG . . . L 5 -16.777 30.386 37.63 1 75.34 ? O6 NAG 521 E 1 HETATM 14 O O7 NAG . . . L 5 -16.038 37.381 40.876 1 81.24 ? O7 NAG 521 E 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 271 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 14 #