data_6M7T
#
_model_server_result.job_id            mdj0EqpYSMol2M_VJYnlrQ 
_model_server_result.datetime_utc      '2024-10-19 17:39:01' 
_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          6m7t 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"I","auth_seq_id":506}' 
#
_entry.id    6M7T 
#
_exptl.entry_id    6M7T 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              92.094 
_entity.id                          8 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            GLYCEROL 
_entity.pdbx_number_of_molecules    3 
_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            6M7T 
_cell.length_a            65.65 
_cell.length_b            80.93 
_cell.length_c            140.38 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6M7T 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    trimeric 
_pdbx_struct_assembly.oligomeric_count      3 
_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 
_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
? 8 H N N 
? 8 I N N 
? 8 J N N 
#
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
covale ? covale1 C O3' DT 2 T DT 3 1_555 C P 02I 3 T 02I 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.608 ? 
covale ? covale2 C O3' 02I 3 T 02I 4 1_555 C P DC 4 T DC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.602 ? 
metalc ? metalc1 A OD1 ASP 16 A ASP 13 1_555 F CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.529 ? 
metalc ? metalc2 A O MET 17 A MET 14 1_555 F CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.09 ? 
metalc ? metalc3 A OD1 ASP 118 A ASP 115 1_555 F CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.187 ? 
metalc ? metalc4 A OD1 ASP 184 A ASP 181 1_555 D NI NI . A NI 501 2_554 ? ? ? ? ? ? ? ? ? ? ? ? 2.224 ? 
metalc ? metalc5 A OD2 ASP 184 A ASP 181 1_555 D NI NI . A NI 501 2_554 ? ? ? ? ? ? ? ? ? ? ? ? 2.72 ? 
metalc ? metalc6 A NE2 HIS 292 A HIS 289 1_555 D NI NI . A NI 501 3_645 ? ? ? ? ? ? ? ? ? ? ? ? 1.941 ? 
metalc ? metalc7 A NE2 HIS 396 A HIS 393 1_555 D NI NI . A NI 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? 
metalc ? metalc8 A NE2 HIS 400 A HIS 397 1_555 D NI NI . A NI 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.004 ? 
metalc ? metalc9 E O1A TTP . A TTP 502 1_555 F CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.39 ? 
metalc ? metalc10 E O1B TTP . A TTP 502 1_555 F CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.341 ? 
metalc ? metalc11 E O2G TTP . A TTP 502 1_555 F CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.312 ? 
hydrog WATSON-CRICK hydrog1 B N1 DG 2 P DG 2 1_555 C N3 DC 10 T DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog2 B N2 DG 2 P DG 2 1_555 C O2 DC 10 T DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog3 B O6 DG 2 P DG 2 1_555 C N4 DC 10 T DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog4 B N3 DT 3 P DT 3 1_555 C N1 DA 9 T DA 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog5 B O4 DT 3 P DT 3 1_555 C N6 DA 9 T DA 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog6 B N1 DG 4 P DG 4 1_555 C N3 DC 8 T DC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog7 B N2 DG 4 P DG 4 1_555 C O2 DC 8 T DC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog8 B O6 DG 4 P DG 4 1_555 C N4 DC 8 T DC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog9 B N3 DT 5 P DT 5 1_555 C N1 DA 7 T DA 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog10 B O4 DT 5 P DT 5 1_555 C N6 DA 7 T DA 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog11 B N1 DG 6 P DG 6 1_555 C N3 DC 6 T DC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog12 B N2 DG 6 P DG 6 1_555 C O2 DC 6 T DC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog13 B O6 DG 6 P DG 6 1_555 C N4 DC 6 T DC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog14 B N1 DA 7 P DA 7 1_555 C N3 DT 5 T DT 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog15 B N6 DA 7 P DA 7 1_555 C O4 DT 5 T DT 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog16 B N1 DG 8 P DG 8 1_555 C N3 DC 4 T DC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog17 B N2 DG 8 P DG 8 1_555 C O2 DC 4 T DC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog18 B O6 DG 8 P DG 8 1_555 C N4 DC 4 T DC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
#
_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 324 n n 
C1 C2 GOL sing 325 n n 
C1 H11 GOL sing 326 n n 
C1 H12 GOL sing 327 n n 
O1 HO1 GOL sing 328 n n 
C2 O2 GOL sing 329 n n 
C2 C3 GOL sing 330 n n 
C2 H2 GOL sing 331 n n 
O2 HO2 GOL sing 332 n n 
C3 O3 GOL sing 333 n n 
C3 H31 GOL sing 334 n n 
C3 H32 GOL sing 335 n n 
O3 HO3 GOL sing 336 n n 
#
_atom_sites.entry_id                     6M7T 
_atom_sites.fract_transf_matrix[1][1]    0.015232 
_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]    0.012356 
_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]    0.007124 
_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 NI A 1 501 452 NI NI . 
E 5 TTP A 1 502 501 TTP TTP . 
F 6 CA A 1 503 2 CA CA . 
G 7 EDO A 1 504 1002 EDO EDO . 
H 8 GOL A 1 505 1003 GOL GOL . 
I 8 GOL A 1 506 1004 GOL GOL . 
J 8 GOL A 1 507 1005 GOL GOL . 
K 9 HOH A 1 601 6 HOH HOH . 
K 9 HOH A 2 602 30 HOH HOH . 
K 9 HOH A 3 603 9 HOH HOH . 
K 9 HOH A 4 604 32 HOH HOH . 
K 9 HOH A 5 605 24 HOH HOH . 
K 9 HOH A 6 606 5 HOH HOH . 
K 9 HOH A 7 607 28 HOH HOH . 
K 9 HOH A 8 608 13 HOH HOH . 
K 9 HOH A 9 609 21 HOH HOH . 
K 9 HOH A 10 610 7 HOH HOH . 
K 9 HOH A 11 611 8 HOH HOH . 
K 9 HOH A 12 612 12 HOH HOH . 
K 9 HOH A 13 613 15 HOH HOH . 
K 9 HOH A 14 614 10 HOH HOH . 
K 9 HOH A 15 615 25 HOH HOH . 
K 9 HOH A 16 616 27 HOH HOH . 
K 9 HOH A 17 617 33 HOH HOH . 
K 9 HOH A 18 618 11 HOH HOH . 
K 9 HOH A 19 619 2 HOH HOH . 
K 9 HOH A 20 620 20 HOH HOH . 
K 9 HOH A 21 621 36 HOH HOH . 
K 9 HOH A 22 622 26 HOH HOH . 
K 9 HOH A 23 623 14 HOH HOH . 
K 9 HOH A 24 624 35 HOH HOH . 
K 9 HOH A 25 625 31 HOH HOH . 
K 9 HOH A 26 626 1 HOH HOH . 
K 9 HOH A 27 627 3 HOH HOH . 
K 9 HOH A 28 628 1 HOH HOH . 
K 9 HOH A 29 629 2 HOH HOH . 
L 9 HOH P 1 101 22 HOH HOH . 
L 9 HOH P 2 102 19 HOH HOH . 
L 9 HOH P 3 103 34 HOH HOH . 
M 9 HOH T 1 101 18 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 . . . I 8 23.728 -17.438 19.003 1 50.32 ? C1 GOL 506 A 1 
HETATM 2 O O1 GOL . . . I 8 22.612 -17.4 19.851 1 71.2 ? O1 GOL 506 A 1 
HETATM 3 C C2 GOL . . . I 8 24.586 -18.655 19.462 1 51.18 ? C2 GOL 506 A 1 
HETATM 4 O O2 GOL . . . I 8 25.895 -18.574 19.029 1 51.43 ? O2 GOL 506 A 1 
HETATM 5 C C3 GOL . . . I 8 23.879 -19.905 18.882 1 48 ? C3 GOL 506 A 1 
HETATM 6 O O3 GOL . . . I 8 22.627 -20.022 19.513 1 50.59 ? O3 GOL 506 A 1 
#
_model_server_stats.io_time_ms              66 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           243 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           6 
#