data_6KDD
#
_model_server_result.job_id            ANa8s2k_TaH4q1z4LvIGoA 
_model_server_result.datetime_utc      '2024-11-10 01:24:26' 
_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          6kdd 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":403}' 
#
_entry.id    6KDD 
#
_exptl.entry_id    6KDD 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              92.094 
_entity.id                          3 
_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         90 
_cell.entry_id            6KDD 
_cell.length_a            50.138 
_cell.length_b            54.895 
_cell.length_c            128.166 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6KDD 
_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    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
? 3 D N N 
? 3 E 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
metalc ? metalc1 A CD2 HIS 67 A HIS 67 1_555 B NI NI . A NI 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.221 ? 
metalc ? metalc2 A ND1 HIS 86 A HIS 86 1_555 C NI NI . A NI 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.145 ? 
metalc ? metalc3 C NI NI . A NI 402 1_555 H O HOH . A HOH 566 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.792 ? 
metalc ? metalc4 C NI NI . A NI 402 1_555 H O HOH . A HOH 587 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.552 ? 
#
_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                     6KDD 
_atom_sites.fract_transf_matrix[1][1]    0.019945 
_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]    0.018217 
_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]    0.007802 
_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
B 2 NI A 1 401 1 NI NI . 
C 2 NI A 1 402 2 NI NI . 
D 3 GOL A 1 403 1 GOL GOL . 
E 3 GOL A 1 404 2 GOL GOL . 
F 4 TRS A 1 405 1 TRS TRS . 
G 4 TRS A 1 406 2 TRS TRS . 
H 5 HOH A 1 501 37 HOH HOH . 
H 5 HOH A 2 502 63 HOH HOH . 
H 5 HOH A 3 503 62 HOH HOH . 
H 5 HOH A 4 504 58 HOH HOH . 
H 5 HOH A 5 505 72 HOH HOH . 
H 5 HOH A 6 506 96 HOH HOH . 
H 5 HOH A 7 507 42 HOH HOH . 
H 5 HOH A 8 508 55 HOH HOH . 
H 5 HOH A 9 509 61 HOH HOH . 
H 5 HOH A 10 510 68 HOH HOH . 
H 5 HOH A 11 511 49 HOH HOH . 
H 5 HOH A 12 512 47 HOH HOH . 
H 5 HOH A 13 513 24 HOH HOH . 
H 5 HOH A 14 514 86 HOH HOH . 
H 5 HOH A 15 515 4 HOH HOH . 
H 5 HOH A 16 516 97 HOH HOH . 
H 5 HOH A 17 517 90 HOH HOH . 
H 5 HOH A 18 518 75 HOH HOH . 
H 5 HOH A 19 519 35 HOH HOH . 
H 5 HOH A 20 520 89 HOH HOH . 
H 5 HOH A 21 521 12 HOH HOH . 
H 5 HOH A 22 522 13 HOH HOH . 
H 5 HOH A 23 523 31 HOH HOH . 
H 5 HOH A 24 524 76 HOH HOH . 
H 5 HOH A 25 525 53 HOH HOH . 
H 5 HOH A 26 526 7 HOH HOH . 
H 5 HOH A 27 527 10 HOH HOH . 
H 5 HOH A 28 528 9 HOH HOH . 
H 5 HOH A 29 529 101 HOH HOH . 
H 5 HOH A 30 530 91 HOH HOH . 
H 5 HOH A 31 531 40 HOH HOH . 
H 5 HOH A 32 532 5 HOH HOH . 
H 5 HOH A 33 533 2 HOH HOH . 
H 5 HOH A 34 534 41 HOH HOH . 
H 5 HOH A 35 535 54 HOH HOH . 
H 5 HOH A 36 536 21 HOH HOH . 
H 5 HOH A 37 537 25 HOH HOH . 
H 5 HOH A 38 538 1 HOH HOH . 
H 5 HOH A 39 539 19 HOH HOH . 
H 5 HOH A 40 540 29 HOH HOH . 
H 5 HOH A 41 541 105 HOH HOH . 
H 5 HOH A 42 542 80 HOH HOH . 
H 5 HOH A 43 543 73 HOH HOH . 
H 5 HOH A 44 544 48 HOH HOH . 
H 5 HOH A 45 545 27 HOH HOH . 
H 5 HOH A 46 546 6 HOH HOH . 
H 5 HOH A 47 547 14 HOH HOH . 
H 5 HOH A 48 548 74 HOH HOH . 
H 5 HOH A 49 549 51 HOH HOH . 
H 5 HOH A 50 550 17 HOH HOH . 
H 5 HOH A 51 551 30 HOH HOH . 
H 5 HOH A 52 552 52 HOH HOH . 
H 5 HOH A 53 553 81 HOH HOH . 
H 5 HOH A 54 554 95 HOH HOH . 
H 5 HOH A 55 555 66 HOH HOH . 
H 5 HOH A 56 556 46 HOH HOH . 
H 5 HOH A 57 557 44 HOH HOH . 
H 5 HOH A 58 558 57 HOH HOH . 
H 5 HOH A 59 559 83 HOH HOH . 
H 5 HOH A 60 560 88 HOH HOH . 
H 5 HOH A 61 561 36 HOH HOH . 
H 5 HOH A 62 562 23 HOH HOH . 
H 5 HOH A 63 563 18 HOH HOH . 
H 5 HOH A 64 564 20 HOH HOH . 
H 5 HOH A 65 565 26 HOH HOH . 
H 5 HOH A 66 566 92 HOH HOH . 
H 5 HOH A 67 567 16 HOH HOH . 
H 5 HOH A 68 568 15 HOH HOH . 
H 5 HOH A 69 569 64 HOH HOH . 
H 5 HOH A 70 570 56 HOH HOH . 
H 5 HOH A 71 571 8 HOH HOH . 
H 5 HOH A 72 572 79 HOH HOH . 
H 5 HOH A 73 573 99 HOH HOH . 
H 5 HOH A 74 574 39 HOH HOH . 
H 5 HOH A 75 575 104 HOH HOH . 
H 5 HOH A 76 576 28 HOH HOH . 
H 5 HOH A 77 577 11 HOH HOH . 
H 5 HOH A 78 578 98 HOH HOH . 
H 5 HOH A 79 579 50 HOH HOH . 
H 5 HOH A 80 580 93 HOH HOH . 
H 5 HOH A 81 581 85 HOH HOH . 
H 5 HOH A 82 582 32 HOH HOH . 
H 5 HOH A 83 583 69 HOH HOH . 
H 5 HOH A 84 584 65 HOH HOH . 
H 5 HOH A 85 585 33 HOH HOH . 
H 5 HOH A 86 586 108 HOH HOH . 
H 5 HOH A 87 587 103 HOH HOH . 
H 5 HOH A 88 588 43 HOH HOH . 
H 5 HOH A 89 589 84 HOH HOH . 
H 5 HOH A 90 590 78 HOH HOH . 
H 5 HOH A 91 591 102 HOH HOH . 
H 5 HOH A 92 592 71 HOH HOH . 
H 5 HOH A 93 593 100 HOH HOH . 
H 5 HOH A 94 594 94 HOH HOH . 
H 5 HOH A 95 595 106 HOH HOH . 
H 5 HOH A 96 596 60 HOH HOH . 
H 5 HOH A 97 597 87 HOH HOH . 
H 5 HOH A 98 598 82 HOH HOH . 
H 5 HOH A 99 599 59 HOH HOH . 
H 5 HOH A 100 600 107 HOH HOH . 
H 5 HOH A 101 601 38 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 . . . D 3 -36.006 13.935 -24.242 1 33.95 ? C1 GOL 403 A 1 
HETATM 2 O O1 GOL . . . D 3 -36.617 12.648 -24.118 1 34.46 ? O1 GOL 403 A 1 
HETATM 3 C C2 GOL . . . D 3 -35.337 14.126 -25.594 1 34.35 ? C2 GOL 403 A 1 
HETATM 4 O O2 GOL . . . D 3 -34.007 14.63 -25.492 1 32.77 ? O2 GOL 403 A 1 
HETATM 5 C C3 GOL . . . D 3 -36.056 15.051 -26.539 1 28.11 ? C3 GOL 403 A 1 
HETATM 6 O O3 GOL . . . D 3 -35.138 15.424 -27.567 1 41.19 ? O3 GOL 403 A 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           311 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           6 
#