data_3GKH
#
_model_server_result.job_id            p2sL9ov1Xc-IPspSfRYpUQ 
_model_server_result.datetime_utc      '2024-11-16 09:43:13' 
_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          3gkh 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":254}' 
#
_entry.id    3GKH 
#
_exptl.entry_id    3GKH 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              92.094 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            GLYCEROL 
_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            3GKH 
_cell.length_a            66.181 
_cell.length_b            66.181 
_cell.length_c            82.644 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3GKH 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        172 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 64' 
#
_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 
_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 
#
_pdbx_entity_branch.entity_id    2 
_pdbx_entity_branch.type         oligosaccharide 
#
_pdbx_entity_branch_link.link_id                     1 
_pdbx_entity_branch_link.details                     ? 
_pdbx_entity_branch_link.entity_id                   2 
_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
2 n B NAG 1 B 1 NAG B 1 NAG 
2 n B NAG 2 B 2 NAG B 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 5 A CYS 25 1_555 A SG CYS 54 A CYS 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf2 A SG CYS 11 A CYS 31 1_555 A SG CYS 22 A CYS 42 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? 
disulf ? disulf3 A SG CYS 43 A CYS 63 1_555 A SG CYS 89 A CYS 109 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? 
disulf ? disulf4 A SG CYS 55 A CYS 75 1_555 A SG CYS 93 A CYS 113 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? 
disulf ? disulf5 A SG CYS 77 A CYS 97 1_555 A SG CYS 218 A CYS 238 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? 
disulf ? disulf6 A SG CYS 80 A CYS 100 1_555 A SG CYS 140 A CYS 160 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? 
disulf ? disulf7 A SG CYS 157 A CYS 177 1_555 A SG CYS 164 A CYS 184 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? 
disulf ? disulf8 A SG CYS 207 A CYS 227 1_555 A SG CYS 223 A CYS 243 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? 
disulf ? disulf9 A SG CYS 220 A CYS 240 1_555 A SG CYS 227 A CYS 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
covale ? covale1 C C1 NAG . A NAG 3 1_555 A ND2 ASN 138 A ASN 158 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? 
covale ? covale2 A ND2 ASN 202 A ASN 222 1_555 B C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? 
covale ? covale3 B O4 NAG . B NAG 1 1_555 B C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.456 ? 
#
_chem_comp.formula           'C3 H8 O3' 
_chem_comp.formula_weight    92.094 
_chem_comp.id                GOL 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              GLYCEROL 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     GLYCERIN;PROPANE-1,2,3-TRIOL 
#
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 O1 GOL sing 129 n n 
C1 C2 GOL sing 130 n n 
C1 H11 GOL sing 131 n n 
C1 H12 GOL sing 132 n n 
O1 HO1 GOL sing 133 n n 
C2 O2 GOL sing 134 n n 
C2 C3 GOL sing 135 n n 
C2 H2 GOL sing 136 n n 
O2 HO2 GOL sing 137 n n 
C3 O3 GOL sing 138 n n 
C3 H31 GOL sing 139 n n 
C3 H32 GOL sing 140 n n 
O3 HO3 GOL sing 141 n n 
#
_atom_sites.entry_id                     3GKH 
_atom_sites.fract_transf_matrix[1][1]    0.01511 
_atom_sites.fract_transf_matrix[1][2]    0.008724 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.017448 
_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]    0.0121 
_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 3 NAG A 1 3 3 NAG NAG . 
D 4 GOL A 1 253 1 GOL GOL . 
E 4 GOL A 1 254 2 GOL GOL . 
F 5 HOH A 1 4 4 HOH HOH . 
F 5 HOH A 2 5 5 HOH HOH . 
F 5 HOH A 3 6 6 HOH HOH . 
F 5 HOH A 4 7 7 HOH HOH . 
F 5 HOH A 5 8 8 HOH HOH . 
F 5 HOH A 6 9 9 HOH HOH . 
F 5 HOH A 7 10 10 HOH HOH . 
F 5 HOH A 8 11 11 HOH HOH . 
F 5 HOH A 9 12 12 HOH HOH . 
F 5 HOH A 10 13 13 HOH HOH . 
F 5 HOH A 11 14 14 HOH HOH . 
F 5 HOH A 12 15 15 HOH HOH . 
F 5 HOH A 13 16 16 HOH HOH . 
F 5 HOH A 14 17 17 HOH HOH . 
F 5 HOH A 15 18 18 HOH HOH . 
F 5 HOH A 16 19 19 HOH HOH . 
F 5 HOH A 17 20 20 HOH HOH . 
F 5 HOH A 18 255 1 HOH HOH . 
F 5 HOH A 19 256 2 HOH HOH . 
F 5 HOH A 20 257 3 HOH HOH . 
F 5 HOH A 21 258 21 HOH HOH . 
F 5 HOH A 22 259 22 HOH HOH . 
F 5 HOH A 23 260 23 HOH HOH . 
F 5 HOH A 24 261 24 HOH HOH . 
F 5 HOH A 25 262 25 HOH HOH . 
F 5 HOH A 26 263 26 HOH HOH . 
F 5 HOH A 27 264 27 HOH HOH . 
F 5 HOH A 28 265 28 HOH HOH . 
F 5 HOH A 29 266 29 HOH HOH . 
F 5 HOH A 30 267 30 HOH HOH . 
F 5 HOH A 31 268 31 HOH HOH . 
F 5 HOH A 32 269 32 HOH HOH . 
F 5 HOH A 33 270 33 HOH HOH . 
F 5 HOH A 34 271 34 HOH HOH . 
F 5 HOH A 35 272 35 HOH HOH . 
F 5 HOH A 36 273 36 HOH HOH . 
F 5 HOH A 37 274 37 HOH HOH . 
F 5 HOH A 38 275 38 HOH HOH . 
F 5 HOH A 39 276 39 HOH HOH . 
F 5 HOH A 40 277 40 HOH HOH . 
F 5 HOH A 41 278 41 HOH HOH . 
F 5 HOH A 42 279 42 HOH HOH . 
F 5 HOH A 43 280 43 HOH HOH . 
F 5 HOH A 44 281 44 HOH HOH . 
F 5 HOH A 45 282 45 HOH HOH . 
F 5 HOH A 46 283 46 HOH HOH . 
F 5 HOH A 47 284 47 HOH HOH . 
F 5 HOH A 48 285 48 HOH HOH . 
F 5 HOH A 49 286 49 HOH HOH . 
F 5 HOH A 50 287 50 HOH HOH . 
F 5 HOH A 51 288 51 HOH HOH . 
F 5 HOH A 52 289 52 HOH HOH . 
F 5 HOH A 53 290 53 HOH HOH . 
F 5 HOH A 54 291 54 HOH HOH . 
F 5 HOH A 55 292 55 HOH HOH . 
F 5 HOH A 56 293 56 HOH HOH . 
F 5 HOH A 57 294 57 HOH HOH . 
F 5 HOH A 58 295 58 HOH HOH . 
F 5 HOH A 59 296 59 HOH HOH . 
F 5 HOH A 60 297 60 HOH HOH . 
F 5 HOH A 61 298 61 HOH HOH . 
F 5 HOH A 62 299 62 HOH HOH . 
F 5 HOH A 63 300 63 HOH HOH . 
F 5 HOH A 64 301 64 HOH HOH . 
F 5 HOH A 65 302 65 HOH HOH . 
F 5 HOH A 66 303 66 HOH HOH . 
F 5 HOH A 67 304 67 HOH HOH . 
F 5 HOH A 68 305 68 HOH HOH . 
F 5 HOH A 69 306 69 HOH HOH . 
F 5 HOH A 70 307 70 HOH HOH . 
F 5 HOH A 71 308 71 HOH HOH . 
F 5 HOH A 72 309 72 HOH HOH . 
F 5 HOH A 73 310 73 HOH HOH . 
F 5 HOH A 74 311 74 HOH HOH . 
F 5 HOH A 75 312 75 HOH HOH . 
F 5 HOH A 76 313 76 HOH HOH . 
F 5 HOH A 77 314 77 HOH HOH . 
F 5 HOH A 78 315 78 HOH HOH . 
F 5 HOH A 79 316 79 HOH HOH . 
F 5 HOH A 80 317 80 HOH HOH . 
F 5 HOH A 81 318 81 HOH HOH . 
F 5 HOH A 82 319 82 HOH HOH . 
F 5 HOH A 83 320 83 HOH HOH . 
F 5 HOH A 84 321 84 HOH HOH . 
F 5 HOH A 85 322 85 HOH HOH . 
F 5 HOH A 86 323 86 HOH HOH . 
F 5 HOH A 87 324 87 HOH HOH . 
F 5 HOH A 88 325 88 HOH HOH . 
F 5 HOH A 89 326 89 HOH HOH . 
F 5 HOH A 90 327 90 HOH HOH . 
F 5 HOH A 91 328 91 HOH HOH . 
F 5 HOH A 92 329 92 HOH HOH . 
F 5 HOH A 93 330 93 HOH HOH . 
F 5 HOH A 94 331 94 HOH HOH . 
F 5 HOH A 95 332 95 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 GOL . . . E 4 -37.5 -29.145 8.189 1 57.1 ? C1 GOL 254 A 1 
HETATM 2 O O1 GOL . . . E 4 -37.858 -30.368 8.809 1 59.6 ? O1 GOL 254 A 1 
HETATM 3 C C2 GOL . . . E 4 -36.832 -29.4 6.834 1 56.98 ? C2 GOL 254 A 1 
HETATM 4 O O2 GOL . . . E 4 -35.682 -28.583 6.675 1 55.03 ? O2 GOL 254 A 1 
HETATM 5 C C3 GOL . . . E 4 -37.833 -29.146 5.703 1 56.94 ? C3 GOL 254 A 1 
HETATM 6 O O3 GOL . . . E 4 -37.181 -29.22 4.444 1 58.34 ? O3 GOL 254 A 1 
#
_model_server_stats.io_time_ms              44 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           270 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           6 
#