data_5E34
#
_model_server_result.job_id            '_ZPxwn12OOrD_YmEF1qK9w' 
_model_server_result.datetime_utc      '2024-11-27 09:27:25' 
_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          5e34 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":1001}' 
#
_entry.id    5E34 
#
_exptl.entry_id    5E34 
_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            5E34 
_cell.length_a            130.824 
_cell.length_b            130.824 
_cell.length_c            133.368 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5E34 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        168 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 6' 
#
_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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2,3 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 2_545 -y,x-y-1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 65.412 -113.296907 0 
3 'crystal symmetry operation' 3_655 -x+y+1,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 130.824 0 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 
#
_pdbx_entity_branch.entity_id    3 
_pdbx_entity_branch.type         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 ? 3 2 1 GAL NAG C1 O1 . O3 HO3 . sing 
2 ? 3 3 2 SIA GAL C2 O2 . O3 HO3 . 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
3 n C NAG 1 C 1 NAG A 3003 NAG 
3 n C GAL 2 C 2 GAL A 3002 GAL 
3 n C SIA 3 C 3 SIA A 3001 SIA 
#
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 8 A CYS 14 1_555 B SG CYS 137 B CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? 
disulf ? disulf2 A SG CYS 46 A CYS 52 1_555 A SG CYS 277 A CYS 277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? 
disulf ? disulf3 A SG CYS 59 A CYS 64 1_555 A SG CYS 71 A CYS 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? 
disulf ? disulf4 A SG CYS 94 A CYS 97 1_555 A SG CYS 138 A CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? 
disulf ? disulf5 A SG CYS 281 A CYS 281 1_555 A SG CYS 305 A CYS 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? 
disulf ? disulf6 B SG CYS 144 B CYS 144 1_555 B SG CYS 148 B CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? 
covale ? covale1 A ND2 ASN 27 A ASN 33 1_555 D C1 NAG . A NAG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? 
covale ? covale2 A ND2 ASN 166 A ASN 167 1_555 E C1 NAG . A NAG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.427 ? 
covale ? covale3 C O3 NAG . C NAG 1 1_555 C C1 GAL . C GAL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? 
covale ? covale4 C O3 GAL . C GAL 2 1_555 C C2 SIA . C SIA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? 
#
_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 261 n n 
C1 O1 NAG sing 262 n n 
C1 O5 NAG sing 263 n n 
C1 H1 NAG sing 264 n n 
C2 C3 NAG sing 265 n n 
C2 N2 NAG sing 266 n n 
C2 H2 NAG sing 267 n n 
C3 C4 NAG sing 268 n n 
C3 O3 NAG sing 269 n n 
C3 H3 NAG sing 270 n n 
C4 C5 NAG sing 271 n n 
C4 O4 NAG sing 272 n n 
C4 H4 NAG sing 273 n n 
C5 C6 NAG sing 274 n n 
C5 O5 NAG sing 275 n n 
C5 H5 NAG sing 276 n n 
C6 O6 NAG sing 277 n n 
C6 H61 NAG sing 278 n n 
C6 H62 NAG sing 279 n n 
C7 C8 NAG sing 280 n n 
C7 N2 NAG sing 281 n n 
C7 O7 NAG doub 282 n n 
C8 H81 NAG sing 283 n n 
C8 H82 NAG sing 284 n n 
C8 H83 NAG sing 285 n n 
N2 HN2 NAG sing 286 n n 
O1 HO1 NAG sing 287 n n 
O3 HO3 NAG sing 288 n n 
O4 HO4 NAG sing 289 n n 
O6 HO6 NAG sing 290 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                     5E34 
_atom_sites.fract_transf_matrix[1][1]    0.007644 
_atom_sites.fract_transf_matrix[1][2]    0.004413 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.008826 
_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]    0.007498 
_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 1001 1001 NAG NAG . 
E 4 NAG A 1 1002 2003 NAG NAG . 
F 5 HOH A 1 1101 13 HOH HOH . 
F 5 HOH A 2 1102 39 HOH HOH . 
F 5 HOH A 3 1103 28 HOH HOH . 
F 5 HOH A 4 1104 63 HOH HOH . 
F 5 HOH A 5 1105 56 HOH HOH . 
F 5 HOH A 6 1106 71 HOH HOH . 
F 5 HOH A 7 1107 31 HOH HOH . 
F 5 HOH A 8 1108 5 HOH HOH . 
F 5 HOH A 9 1109 35 HOH HOH . 
F 5 HOH A 10 1110 53 HOH HOH . 
F 5 HOH A 11 1111 38 HOH HOH . 
F 5 HOH A 12 1112 2 HOH HOH . 
F 5 HOH A 13 1113 44 HOH HOH . 
F 5 HOH A 14 1114 24 HOH HOH . 
F 5 HOH A 15 1115 3 HOH HOH . 
F 5 HOH A 16 1116 69 HOH HOH . 
F 5 HOH A 17 1117 8 HOH HOH . 
F 5 HOH A 18 1118 50 HOH HOH . 
F 5 HOH A 19 1119 10 HOH HOH . 
F 5 HOH A 20 1120 42 HOH HOH . 
F 5 HOH A 21 1121 26 HOH HOH . 
F 5 HOH A 22 1122 22 HOH HOH . 
F 5 HOH A 23 1123 20 HOH HOH . 
F 5 HOH A 24 1124 25 HOH HOH . 
F 5 HOH A 25 1125 47 HOH HOH . 
F 5 HOH A 26 1126 70 HOH HOH . 
F 5 HOH A 27 1127 11 HOH HOH . 
F 5 HOH A 28 1128 78 HOH HOH . 
F 5 HOH A 29 1129 62 HOH HOH . 
F 5 HOH A 30 1130 55 HOH HOH . 
F 5 HOH A 31 1131 36 HOH HOH . 
F 5 HOH A 32 1132 19 HOH HOH . 
F 5 HOH A 33 1133 16 HOH HOH . 
F 5 HOH A 34 1134 21 HOH HOH . 
F 5 HOH A 35 1135 85 HOH HOH . 
F 5 HOH A 36 1136 9 HOH HOH . 
F 5 HOH A 37 1137 27 HOH HOH . 
F 5 HOH A 38 1138 83 HOH HOH . 
F 5 HOH A 39 1139 54 HOH HOH . 
F 5 HOH A 40 1140 80 HOH HOH . 
F 5 HOH A 41 1141 68 HOH HOH . 
F 5 HOH A 42 1142 4 HOH HOH . 
F 5 HOH A 43 1143 6 HOH HOH . 
F 5 HOH A 44 1144 33 HOH HOH . 
F 5 HOH A 45 1145 73 HOH HOH . 
F 5 HOH A 46 1146 23 HOH HOH . 
F 5 HOH A 47 1147 82 HOH HOH . 
F 5 HOH A 48 1148 14 HOH HOH . 
F 5 HOH A 49 1149 12 HOH HOH . 
F 5 HOH A 50 1150 17 HOH HOH . 
F 5 HOH A 51 1151 34 HOH HOH . 
F 5 HOH A 52 1152 74 HOH HOH . 
F 5 HOH A 53 1153 61 HOH HOH . 
F 5 HOH A 54 1154 77 HOH HOH . 
F 5 HOH A 55 1155 60 HOH HOH . 
F 5 HOH A 56 1156 30 HOH HOH . 
F 5 HOH A 57 1157 81 HOH HOH . 
F 5 HOH A 58 1158 87 HOH HOH . 
F 5 HOH A 59 1159 45 HOH HOH . 
F 5 HOH A 60 1160 40 HOH HOH . 
F 5 HOH A 61 1161 43 HOH HOH . 
F 5 HOH A 62 1162 86 HOH HOH . 
F 5 HOH A 63 1163 51 HOH HOH . 
F 5 HOH A 64 1164 72 HOH HOH . 
F 5 HOH A 65 1165 75 HOH HOH . 
F 5 HOH A 66 1166 58 HOH HOH . 
F 5 HOH A 67 1167 84 HOH HOH . 
F 5 HOH A 68 1168 64 HOH HOH . 
F 5 HOH A 69 1169 65 HOH HOH . 
F 5 HOH A 70 1170 90 HOH HOH . 
G 5 HOH B 1 201 37 HOH HOH . 
G 5 HOH B 2 202 57 HOH HOH . 
G 5 HOH B 3 203 29 HOH HOH . 
G 5 HOH B 4 204 52 HOH HOH . 
G 5 HOH B 5 205 7 HOH HOH . 
G 5 HOH B 6 206 67 HOH HOH . 
G 5 HOH B 7 207 59 HOH HOH . 
G 5 HOH B 8 208 15 HOH HOH . 
G 5 HOH B 9 209 41 HOH HOH . 
G 5 HOH B 10 210 18 HOH HOH . 
G 5 HOH B 11 211 1 HOH HOH . 
G 5 HOH B 12 212 32 HOH HOH . 
G 5 HOH B 13 213 49 HOH HOH . 
G 5 HOH B 14 214 46 HOH HOH . 
G 5 HOH B 15 215 79 HOH HOH . 
G 5 HOH B 16 216 89 HOH HOH . 
G 5 HOH B 17 217 88 HOH HOH . 
G 5 HOH B 18 218 48 HOH HOH . 
G 5 HOH B 19 219 76 HOH HOH . 
G 5 HOH B 20 220 66 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 81.499 -21.236 -53.5 1 94.49 ? C1 NAG 1001 A 1 
HETATM 2 C C2 NAG . . . D 4 82.977 -21.602 -53.303 1 98.12 ? C2 NAG 1001 A 1 
HETATM 3 C C3 NAG . . . D 4 83.498 -21.031 -51.98 1 100.03 ? C3 NAG 1001 A 1 
HETATM 4 C C4 NAG . . . D 4 83.201 -19.541 -51.866 1 101.59 ? C4 NAG 1001 A 1 
HETATM 5 C C5 NAG . . . D 4 81.716 -19.272 -52.108 1 95.08 ? C5 NAG 1001 A 1 
HETATM 6 C C6 NAG . . . D 4 81.373 -17.799 -52.135 1 92.23 ? C6 NAG 1001 A 1 
HETATM 7 C C7 NAG . . . D 4 84.086 -23.644 -54.11 1 99.39 ? C7 NAG 1001 A 1 
HETATM 8 C C8 NAG . . . D 4 84.131 -25.141 -54.03 1 90.65 ? C8 NAG 1001 A 1 
HETATM 9 N N2 NAG . . . D 4 83.164 -23.042 -53.347 1 97.83 ? N2 NAG 1001 A 1 
HETATM 10 O O3 NAG . . . D 4 84.903 -21.256 -51.889 1 99.81 ? O3 NAG 1001 A 1 
HETATM 11 O O4 NAG . . . D 4 83.567 -19.071 -50.571 1 102.81 ? O4 NAG 1001 A 1 
HETATM 12 O O5 NAG . . . D 4 81.327 -19.808 -53.383 1 97.38 ? O5 NAG 1001 A 1 
HETATM 13 O O6 NAG . . . D 4 81.981 -17.132 -53.234 1 92.9 ? O6 NAG 1001 A 1 
HETATM 14 O O7 NAG . . . D 4 84.85 -23.007 -54.832 1 102.4 ? O7 NAG 1001 A 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           279 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           14 
#