data_5HVW
#
_model_server_result.job_id            p0GdiShjGMbeAphbYXd2YA 
_model_server_result.datetime_utc      '2024-10-12 14:29:22' 
_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          5hvw 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":512}' 
#
_entry.id    5HVW 
#
_exptl.entry_id    5HVW 
_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    1 
_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            5HVW 
_cell.length_a            121.379 
_cell.length_b            121.379 
_cell.length_c            99.729 
_cell.Z_PDB               18 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5HVW 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        155 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'H 3 2' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA hexameric 6 software_defined_assembly 1 
PISA monomeric 1 author_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,C,D,E,F 1 1,2,3,4,5,6 
A,B,C,D,E,F 2 1 
#
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_555 -y,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 0 0 0 
3 'crystal symmetry operation' 3_555 -x+y,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 0 0 0 
4 'crystal symmetry operation' 4_555 y,x,-z -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 0 
5 'crystal symmetry operation' 5_555 x-y,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 
6 'crystal symmetry operation' 6_555 -x,-x+y,-z -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 0 0 0 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      4 
_struct_asym.id                             E 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
_pdbx_entity_branch.entity_id    2 
_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 ? 2 2 1 NAG NAG C1 O1 . O4 HO4 . sing 
2 ? 2 3 2 BMA NAG C1 O1 . O4 HO4 . sing 
3 ? 2 4 3 MAN BMA C1 O1 . O6 HO6 . sing 
4 ? 2 5 4 NAG MAN C1 O1 . O2 HO2 . sing 
5 ? 2 6 5 GAL NAG C1 O1 . O4 HO4 . sing 
6 ? 2 7 3 MAN BMA C1 O1 . O3 HO3 . sing 
7 ? 2 8 7 NAG MAN C1 O1 . O2 HO2 . sing 
8 ? 2 9 1 FUC NAG C1 O1 . O6 HO6 . 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 501 NAG 
2 n B NAG 2 B 2 NAG A 502 NAG 
2 n B BMA 3 B 3 BMA A 503 BMA 
2 n B MAN 4 B 4 MAN A 504 MAN 
2 n B NAG 5 B 5 NAG A 505 NAG 
2 n B GAL 6 B 6 GAL A 509 GAL 
2 n B MAN 7 B 7 MAN A 506 MAN 
2 n B NAG 8 B 8 NAG A 507 NAG 
2 n B FUC 9 B 9 FUC A 508 FUC 
#
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 27 A CYS 261 1_555 A SG CYS 87 A CYS 321 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? 
disulf ? disulf2 A SG CYS 133 A CYS 367 1_555 A SG CYS 191 A CYS 425 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? 
covale ? covale1 A ND2 ASN 63 A ASN 297 1_555 B C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? 
covale ? covale2 B O4 NAG . B NAG 1 1_555 B C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? 
covale ? covale3 B O6 NAG . B NAG 1 1_555 B C1 FUC . B FUC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? 
covale ? covale4 B O4 NAG . B NAG 2 1_555 B C1 BMA . B BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? 
covale ? covale5 B O6 BMA . B BMA 3 1_555 B C1 MAN . B MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? 
covale ? covale6 B O3 BMA . B BMA 3 1_555 B C1 MAN . B MAN 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? 
covale ? covale7 B O2 MAN . B MAN 4 1_555 B C1 NAG . B NAG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.429 ? 
covale ? covale8 B O4 NAG . B NAG 5 1_555 B C1 GAL . B GAL 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? 
covale ? covale9 B O2 MAN . B MAN 7 1_555 B C1 NAG . B NAG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? 
metalc ? metalc1 A NE2 HIS 51 A HIS 285 1_555 C ZN ZN . A ZN 510 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.375 ? 
metalc ? metalc2 A NE2 HIS 51 A HIS 285 1_555 C ZN ZN . A ZN 510 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.375 ? 
metalc ? metalc3 A NE2 HIS 76 A HIS 310 1_555 D ZN ZN . A ZN 511 4_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.205 ? 
metalc ? metalc4 A NE2 HIS 199 A HIS 433 1_555 D ZN ZN . A ZN 511 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.125 ? 
metalc ? metalc5 A NE2 HIS 201 A HIS 435 1_555 D ZN ZN . A ZN 511 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.937 ? 
metalc ? metalc6 C ZN ZN . A ZN 510 1_555 F O HOH . A HOH 653 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.965 ? 
metalc ? metalc7 C ZN ZN . A ZN 510 1_555 F O HOH . A HOH 653 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.965 ? 
metalc ? metalc8 D ZN ZN . A ZN 511 1_555 F O HOH . A HOH 671 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.186 ? 
#
_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 
#
_atom_sites.entry_id                     5HVW 
_atom_sites.fract_transf_matrix[1][1]    0.008239 
_atom_sites.fract_transf_matrix[1][2]    0.004757 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.009513 
_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]    0.010027 
_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 ZN A 1 510 1 ZN ZN . 
D 3 ZN A 1 511 2 ZN ZN . 
E 4 GOL A 1 512 1 GOL GOL . 
F 5 HOH A 1 601 2 HOH HOH . 
F 5 HOH A 2 602 6 HOH HOH . 
F 5 HOH A 3 603 80 HOH HOH . 
F 5 HOH A 4 604 57 HOH HOH . 
F 5 HOH A 5 605 10 HOH HOH . 
F 5 HOH A 6 606 71 HOH HOH . 
F 5 HOH A 7 607 36 HOH HOH . 
F 5 HOH A 8 608 76 HOH HOH . 
F 5 HOH A 9 609 12 HOH HOH . 
F 5 HOH A 10 610 47 HOH HOH . 
F 5 HOH A 11 611 32 HOH HOH . 
F 5 HOH A 12 612 19 HOH HOH . 
F 5 HOH A 13 613 72 HOH HOH . 
F 5 HOH A 14 614 25 HOH HOH . 
F 5 HOH A 15 615 13 HOH HOH . 
F 5 HOH A 16 616 3 HOH HOH . 
F 5 HOH A 17 617 23 HOH HOH . 
F 5 HOH A 18 618 56 HOH HOH . 
F 5 HOH A 19 619 8 HOH HOH . 
F 5 HOH A 20 620 48 HOH HOH . 
F 5 HOH A 21 621 22 HOH HOH . 
F 5 HOH A 22 622 51 HOH HOH . 
F 5 HOH A 23 623 27 HOH HOH . 
F 5 HOH A 24 624 55 HOH HOH . 
F 5 HOH A 25 625 20 HOH HOH . 
F 5 HOH A 26 626 9 HOH HOH . 
F 5 HOH A 27 627 52 HOH HOH . 
F 5 HOH A 28 628 16 HOH HOH . 
F 5 HOH A 29 629 7 HOH HOH . 
F 5 HOH A 30 630 69 HOH HOH . 
F 5 HOH A 31 631 21 HOH HOH . 
F 5 HOH A 32 632 34 HOH HOH . 
F 5 HOH A 33 633 5 HOH HOH . 
F 5 HOH A 34 634 53 HOH HOH . 
F 5 HOH A 35 635 24 HOH HOH . 
F 5 HOH A 36 636 15 HOH HOH . 
F 5 HOH A 37 637 28 HOH HOH . 
F 5 HOH A 38 638 65 HOH HOH . 
F 5 HOH A 39 639 35 HOH HOH . 
F 5 HOH A 40 640 33 HOH HOH . 
F 5 HOH A 41 641 17 HOH HOH . 
F 5 HOH A 42 642 29 HOH HOH . 
F 5 HOH A 43 643 54 HOH HOH . 
F 5 HOH A 44 644 31 HOH HOH . 
F 5 HOH A 45 645 73 HOH HOH . 
F 5 HOH A 46 646 37 HOH HOH . 
F 5 HOH A 47 647 61 HOH HOH . 
F 5 HOH A 48 648 60 HOH HOH . 
F 5 HOH A 49 649 64 HOH HOH . 
F 5 HOH A 50 650 38 HOH HOH . 
F 5 HOH A 51 651 4 HOH HOH . 
F 5 HOH A 52 652 39 HOH HOH . 
F 5 HOH A 53 653 1 HOH HOH . 
F 5 HOH A 54 654 43 HOH HOH . 
F 5 HOH A 55 655 42 HOH HOH . 
F 5 HOH A 56 656 62 HOH HOH . 
F 5 HOH A 57 657 11 HOH HOH . 
F 5 HOH A 58 658 74 HOH HOH . 
F 5 HOH A 59 659 26 HOH HOH . 
F 5 HOH A 60 660 14 HOH HOH . 
F 5 HOH A 61 661 68 HOH HOH . 
F 5 HOH A 62 662 50 HOH HOH . 
F 5 HOH A 63 663 40 HOH HOH . 
F 5 HOH A 64 664 81 HOH HOH . 
F 5 HOH A 65 665 18 HOH HOH . 
F 5 HOH A 66 666 41 HOH HOH . 
F 5 HOH A 67 667 63 HOH HOH . 
F 5 HOH A 68 668 49 HOH HOH . 
F 5 HOH A 69 669 58 HOH HOH . 
F 5 HOH A 70 670 67 HOH HOH . 
F 5 HOH A 71 671 30 HOH HOH . 
F 5 HOH A 72 672 59 HOH HOH . 
F 5 HOH A 73 673 77 HOH HOH . 
F 5 HOH A 74 674 70 HOH HOH . 
F 5 HOH A 75 675 78 HOH HOH . 
F 5 HOH A 76 676 46 HOH HOH . 
F 5 HOH A 77 677 79 HOH HOH . 
F 5 HOH A 78 678 66 HOH HOH . 
F 5 HOH A 79 679 75 HOH HOH . 
F 5 HOH A 80 680 44 HOH HOH . 
F 5 HOH A 81 681 45 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 1.966 35.345 9.833 1 75.66 ? C1 GOL 512 A 1 
HETATM 2 O O1 GOL . . . E 4 3.139 35.84 9.141 1 63.35 ? O1 GOL 512 A 1 
HETATM 3 C C2 GOL . . . E 4 0.682 35.429 8.977 1 76.01 ? C2 GOL 512 A 1 
HETATM 4 O O2 GOL . . . E 4 0.055 36.706 9.191 1 60.17 ? O2 GOL 512 A 1 
HETATM 5 C C3 GOL . . . E 4 -0.408 34.373 9.281 1 73.4 ? C3 GOL 512 A 1 
HETATM 6 O O3 GOL . . . E 4 0.079 33.043 9.454 1 77.27 ? O3 GOL 512 A 1 
#
_model_server_stats.io_time_ms              17 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           316 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           6 
#