data_3ZR6 # _model_server_result.job_id wWCdcZw7wzKOLhRD3lyy2A _model_server_result.datetime_utc '2024-11-28 00:34:05' _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 3zr6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":701}' # _entry.id 3ZR6 # _exptl.entry_id 3ZR6 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 4 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 2 _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 120 _cell.entry_id 3ZR6 _cell.length_a 249.548 _cell.length_b 249.548 _cell.length_c 77.456 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3ZR6 _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'H 3 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 ? 4 D N N ? 4 E N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 2 oligosaccharide 3 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 ? 2 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 3 3 2 BMA 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 2 n B NAG 1 B 1 NAG A 1363 NAG 2 n B NAG 2 B 2 NAG A 2363 NAG 3 n C NAG 1 C 1 NAG A 1542 NAG 3 n C NAG 2 C 2 NAG A 2542 NAG 3 n C BMA 3 C 3 BMA A 3542 BMA # 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 259 A CYS 271 1_555 A SG CYS 366 A CYS 378 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? covale ? covale1 A ND2 ASN 272 A ASN 284 1_555 D C1 NAG . A NAG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale2 A ND2 ASN 351 A ASN 363 1_555 B C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale3 A ND2 ASN 375 A ASN 387 1_555 E C1 NAG . A NAG 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.467 ? covale ? covale4 A ND2 ASN 530 A ASN 542 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale5 B O4 NAG . B NAG 1 1_555 B C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale6 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale7 C O4 NAG . C NAG 2 1_555 C C1 BMA . C BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.472 ? metalc ? metalc1 A O ASP 465 A ASP 477 1_555 G CA CA . A CA 709 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.038 ? metalc ? metalc2 A OD1 ASN 467 A ASN 479 1_555 G CA CA . A CA 709 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.665 ? metalc ? metalc3 A O PHE 499 A PHE 511 1_555 G CA CA . A CA 709 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.538 ? metalc ? metalc4 A OD1 ASP 648 A ASP 660 1_555 G CA CA . A CA 709 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.674 ? metalc ? metalc5 A OD2 ASP 648 A ASP 660 1_555 G CA CA . A CA 709 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.958 ? metalc ? metalc6 G CA CA . A CA 709 1_555 H O HOH . A HOH 4005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.986 ? metalc ? metalc7 G CA CA . A CA 709 1_555 H O HOH . A HOH 4024 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.63 ? # _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 285 n n C1 O1 NAG sing 286 n n C1 O5 NAG sing 287 n n C1 H1 NAG sing 288 n n C2 C3 NAG sing 289 n n C2 N2 NAG sing 290 n n C2 H2 NAG sing 291 n n C3 C4 NAG sing 292 n n C3 O3 NAG sing 293 n n C3 H3 NAG sing 294 n n C4 C5 NAG sing 295 n n C4 O4 NAG sing 296 n n C4 H4 NAG sing 297 n n C5 C6 NAG sing 298 n n C5 O5 NAG sing 299 n n C5 H5 NAG sing 300 n n C6 O6 NAG sing 301 n n C6 H61 NAG sing 302 n n C6 H62 NAG sing 303 n n C7 C8 NAG sing 304 n n C7 N2 NAG sing 305 n n C7 O7 NAG doub 306 n n C8 H81 NAG sing 307 n n C8 H82 NAG sing 308 n n C8 H83 NAG sing 309 n n N2 HN2 NAG sing 310 n n O1 HO1 NAG sing 311 n n O3 HO3 NAG sing 312 n n O4 HO4 NAG sing 313 n n O6 HO6 NAG sing 314 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 3ZR6 _atom_sites.fract_transf_matrix[1][1] 0.004007 _atom_sites.fract_transf_matrix[1][2] 0.002314 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.004627 _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] 0.012911 _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 D 4 NAG A 1 701 1284 NAG NAG . E 4 NAG A 1 704 1387 NAG NAG . F 5 GAL A 1 708 1669 GAL GAL . G 6 CA A 1 709 1670 CA CA . H 7 HOH A 1 4001 4001 HOH HOH . H 7 HOH A 2 4002 4090 HOH HOH . H 7 HOH A 3 4003 4098 HOH HOH . H 7 HOH A 4 4004 4137 HOH HOH . H 7 HOH A 5 4005 4108 HOH HOH . H 7 HOH A 6 4006 4074 HOH HOH . H 7 HOH A 7 4007 4101 HOH HOH . H 7 HOH A 8 4008 4071 HOH HOH . H 7 HOH A 9 4009 4118 HOH HOH . H 7 HOH A 10 4010 4021 HOH HOH . H 7 HOH A 11 4011 4066 HOH HOH . H 7 HOH A 12 4012 4106 HOH HOH . H 7 HOH A 13 4013 4062 HOH HOH . H 7 HOH A 14 4014 4009 HOH HOH . H 7 HOH A 15 4015 4015 HOH HOH . H 7 HOH A 16 4016 4019 HOH HOH . H 7 HOH A 17 4017 4126 HOH HOH . H 7 HOH A 18 4018 4003 HOH HOH . H 7 HOH A 19 4019 4112 HOH HOH . H 7 HOH A 20 4020 4131 HOH HOH . H 7 HOH A 21 4021 4129 HOH HOH . H 7 HOH A 22 4022 4018 HOH HOH . H 7 HOH A 23 4023 4110 HOH HOH . H 7 HOH A 24 4024 4113 HOH HOH . H 7 HOH A 25 4025 4081 HOH HOH . H 7 HOH A 26 4026 4116 HOH HOH . H 7 HOH A 27 4027 4027 HOH HOH . H 7 HOH A 28 4028 4105 HOH HOH . H 7 HOH A 29 4029 4122 HOH HOH . H 7 HOH A 30 4030 4022 HOH HOH . H 7 HOH A 31 4031 4135 HOH HOH . H 7 HOH A 32 4032 4017 HOH HOH . H 7 HOH A 33 4033 4007 HOH HOH . H 7 HOH A 34 4034 4048 HOH HOH . H 7 HOH A 35 4035 4125 HOH HOH . H 7 HOH A 36 4036 4013 HOH HOH . H 7 HOH A 37 4037 4050 HOH HOH . H 7 HOH A 38 4038 4057 HOH HOH . H 7 HOH A 39 4039 4043 HOH HOH . H 7 HOH A 40 4040 4058 HOH HOH . H 7 HOH A 41 4041 4025 HOH HOH . H 7 HOH A 42 4042 4026 HOH HOH . H 7 HOH A 43 4043 4005 HOH HOH . H 7 HOH A 44 4044 4061 HOH HOH . H 7 HOH A 45 4045 4040 HOH HOH . H 7 HOH A 46 4046 4079 HOH HOH . H 7 HOH A 47 4047 4006 HOH HOH . H 7 HOH A 48 4048 4045 HOH HOH . H 7 HOH A 49 4049 4051 HOH HOH . H 7 HOH A 50 4050 4008 HOH HOH . H 7 HOH A 51 4051 4002 HOH HOH . H 7 HOH A 52 4052 4023 HOH HOH . H 7 HOH A 53 4053 4063 HOH HOH . H 7 HOH A 54 4054 4014 HOH HOH . H 7 HOH A 55 4055 4103 HOH HOH . H 7 HOH A 56 4056 4075 HOH HOH . H 7 HOH A 57 4057 4011 HOH HOH . H 7 HOH A 58 4058 4114 HOH HOH . H 7 HOH A 59 4059 4072 HOH HOH . H 7 HOH A 60 4060 4020 HOH HOH . H 7 HOH A 61 4061 4100 HOH HOH . H 7 HOH A 62 4062 4115 HOH HOH . H 7 HOH A 63 4063 4123 HOH HOH . H 7 HOH A 64 4064 4010 HOH HOH . H 7 HOH A 65 4065 4067 HOH HOH . H 7 HOH A 66 4066 4093 HOH HOH . H 7 HOH A 67 4067 4089 HOH HOH . H 7 HOH A 68 4068 4077 HOH HOH . H 7 HOH A 69 4069 4028 HOH HOH . H 7 HOH A 70 4070 4041 HOH HOH . H 7 HOH A 71 4071 4127 HOH HOH . H 7 HOH A 72 4072 4088 HOH HOH . H 7 HOH A 73 4073 4136 HOH HOH . H 7 HOH A 74 4074 4049 HOH HOH . H 7 HOH A 75 4075 4036 HOH HOH . H 7 HOH A 76 4076 4076 HOH HOH . H 7 HOH A 77 4077 4099 HOH HOH . H 7 HOH A 78 4078 4070 HOH HOH . H 7 HOH A 79 4079 4029 HOH HOH . H 7 HOH A 80 4080 4042 HOH HOH . H 7 HOH A 81 4081 4082 HOH HOH . H 7 HOH A 82 4082 4052 HOH HOH . H 7 HOH A 83 4083 4024 HOH HOH . H 7 HOH A 84 4084 4107 HOH HOH . H 7 HOH A 85 4085 4084 HOH HOH . H 7 HOH A 86 4086 4083 HOH HOH . H 7 HOH A 87 4087 4133 HOH HOH . H 7 HOH A 88 4088 4111 HOH HOH . H 7 HOH A 89 4089 4091 HOH HOH . H 7 HOH A 90 4090 4064 HOH HOH . H 7 HOH A 91 4091 4097 HOH HOH . H 7 HOH A 92 4092 4034 HOH HOH . H 7 HOH A 93 4093 4038 HOH HOH . H 7 HOH A 94 4094 4095 HOH HOH . H 7 HOH A 95 4095 4031 HOH HOH . H 7 HOH A 96 4096 4121 HOH HOH . H 7 HOH A 97 4097 4053 HOH HOH . H 7 HOH A 98 4098 4055 HOH HOH . H 7 HOH A 99 4099 4134 HOH HOH . H 7 HOH A 100 4100 4132 HOH HOH . H 7 HOH A 101 4101 4060 HOH HOH . H 7 HOH A 102 4102 4128 HOH HOH . H 7 HOH A 103 4103 4065 HOH HOH . H 7 HOH A 104 4104 4104 HOH HOH . H 7 HOH A 105 4105 4096 HOH HOH . H 7 HOH A 106 4106 4030 HOH HOH . H 7 HOH A 107 4107 4094 HOH HOH . H 7 HOH A 108 4108 4012 HOH HOH . H 7 HOH A 109 4109 4044 HOH HOH . H 7 HOH A 110 4110 4032 HOH HOH . H 7 HOH A 111 4111 4086 HOH HOH . H 7 HOH A 112 4112 4124 HOH HOH . H 7 HOH A 113 4113 4047 HOH HOH . H 7 HOH A 114 4114 4119 HOH HOH . H 7 HOH A 115 4115 4080 HOH HOH . H 7 HOH A 116 4116 4068 HOH HOH . H 7 HOH A 117 4117 4039 HOH HOH . H 7 HOH A 118 4118 4092 HOH HOH . H 7 HOH A 119 4119 4046 HOH HOH . H 7 HOH A 120 4120 4120 HOH HOH . H 7 HOH A 121 4121 4056 HOH HOH . H 7 HOH A 122 4122 4109 HOH HOH . H 7 HOH A 123 4123 4004 HOH HOH . H 7 HOH A 124 4124 4087 HOH HOH . H 7 HOH A 125 4125 4054 HOH HOH . H 7 HOH A 126 4126 4035 HOH HOH . H 7 HOH A 127 4127 4102 HOH HOH . H 7 HOH A 128 4128 4069 HOH HOH . H 7 HOH A 129 4129 4130 HOH HOH . H 7 HOH A 130 4130 4085 HOH HOH . H 7 HOH A 131 4131 4138 HOH HOH . H 7 HOH A 132 4132 4078 HOH HOH . H 7 HOH A 133 4133 4073 HOH HOH . H 7 HOH A 134 4134 4059 HOH HOH . H 7 HOH A 135 4135 4117 HOH HOH . H 7 HOH A 136 4136 4139 HOH HOH . H 7 HOH A 137 4137 4037 HOH HOH . H 7 HOH A 138 4138 4033 HOH HOH . H 7 HOH A 139 4139 4016 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 . . . D 4 73.152 104.474 -2.008 1 86.47 ? C1 NAG 701 A 1 HETATM 2 C C2 NAG . . . D 4 72.327 105.593 -2.635 1 88.45 ? C2 NAG 701 A 1 HETATM 3 C C3 NAG . . . D 4 72.328 105.647 -4.17 1 89.08 ? C3 NAG 701 A 1 HETATM 4 C C4 NAG . . . D 4 73.708 105.35 -4.747 1 90.01 ? C4 NAG 701 A 1 HETATM 5 C C5 NAG . . . D 4 74.216 104.067 -4.087 1 88.71 ? C5 NAG 701 A 1 HETATM 6 C C6 NAG . . . D 4 75.561 103.613 -4.643 1 88.8 ? C6 NAG 701 A 1 HETATM 7 C C7 NAG . . . D 4 70.338 106.297 -1.411 1 89.63 ? C7 NAG 701 A 1 HETATM 8 C C8 NAG . . . D 4 71.115 107.468 -0.859 1 89.41 ? C8 NAG 701 A 1 HETATM 9 N N2 NAG . . . D 4 70.974 105.405 -2.169 1 89.09 ? N2 NAG 701 A 1 HETATM 10 O O3 NAG . . . D 4 71.892 106.919 -4.61 1 87.69 ? O3 NAG 701 A 1 HETATM 11 O O4 NAG . . . D 4 73.666 105.262 -6.17 1 91.64 ? O4 NAG 701 A 1 HETATM 12 O O5 NAG . . . D 4 74.361 104.253 -2.693 1 86.61 ? O5 NAG 701 A 1 HETATM 13 O O6 NAG . . . D 4 76.195 102.807 -3.67 1 87.46 ? O6 NAG 701 A 1 HETATM 14 O O7 NAG . . . D 4 69.14 106.173 -1.162 1 89.02 ? O7 NAG 701 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 221 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 14 #