data_5GTD
#
_model_server_result.job_id            77Oqoqoc-M8HU54KEpcMGw 
_model_server_result.datetime_utc      '2025-01-11 22:25:24' 
_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          5gtd 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"M","auth_seq_id":505}' 
#
_entry.id    5GTD 
#
_exptl.entry_id    5GTD 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              222.194 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            2-SUCCINYLBENZOATE 
_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            5GTD 
_cell.length_a            121.814 
_cell.length_b            121.814 
_cell.length_c            98.563 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5GTD 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        78 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 43' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_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,N,O 
_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
? 5 H N N 
? 5 M 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 G P AMP . A AMP 505 1_555 H O5 OSB . A OSB 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.595 ? 
covale ? covale2 L P AMP . B AMP 504 1_555 M O4 OSB . B OSB 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.596 ? 
metalc ? metalc1 B O PRO 8 B PRO 6 1_555 J MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.902 ? 
metalc ? metalc2 B OE1 GLN 13 B GLN 11 1_555 J MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.851 ? 
#
_chem_comp.formula           'C11 H10 O5' 
_chem_comp.formula_weight    222.194 
_chem_comp.id                OSB 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              2-SUCCINYLBENZOATE 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     O-SUCCINYLBENZOATE 
#
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
O1 C7 OSB sing 286 n n 
O1 HO1 OSB sing 287 n n 
O2 C7 OSB doub 288 n n 
C7 C2 OSB sing 289 n n 
C6 C5 OSB doub 290 n y 
C6 C1 OSB sing 291 n y 
C6 H61 OSB sing 292 n n 
C5 C4 OSB sing 293 n y 
C5 H51 OSB sing 294 n n 
C4 C3 OSB doub 295 n y 
C4 H41 OSB sing 296 n n 
C3 C2 OSB sing 297 n y 
C3 H31 OSB sing 298 n n 
C2 C1 OSB doub 299 n y 
C1 C8 OSB sing 300 n n 
C8 C9 OSB sing 301 n n 
C8 O3 OSB doub 302 n n 
C9 C10 OSB sing 303 n n 
C9 H91 OSB sing 304 n n 
C9 H92 OSB sing 305 n n 
C10 C11 OSB sing 306 n n 
C10 H101 OSB sing 307 n n 
C10 H102 OSB sing 308 n n 
C11 O4 OSB doub 309 n n 
C11 O5 OSB sing 310 n n 
O5 HO5 OSB sing 311 n n 
#
_atom_sites.entry_id                     5GTD 
_atom_sites.fract_transf_matrix[1][1]    0.008209 
_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]    0.008209 
_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]    0.010146 
_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 2 CL A 1 501 2 CL CL . 
D 2 CL A 1 502 5 CL CL . 
E 2 CL A 1 503 6 CL CL . 
F 3 PEG A 1 504 1 PEG PEG . 
G 4 AMP A 1 505 500 AMP DRG . 
H 5 OSB A 1 506 500 OSB DRG . 
I 2 CL B 1 501 3 CL CL . 
J 6 MG B 1 502 2 MG MG . 
K 7 IMD B 1 503 1 IMD IMD . 
L 4 AMP B 1 504 500 AMP DRG . 
M 5 OSB B 1 505 500 OSB DRG . 
N 8 HOH A 1 601 18 HOH HOH . 
N 8 HOH A 2 602 17 HOH HOH . 
N 8 HOH A 3 603 11 HOH HOH . 
N 8 HOH A 4 604 7 HOH HOH . 
N 8 HOH A 5 605 8 HOH HOH . 
N 8 HOH A 6 606 36 HOH HOH . 
N 8 HOH A 7 607 10 HOH HOH . 
N 8 HOH A 8 608 6 HOH HOH . 
N 8 HOH A 9 609 12 HOH HOH . 
N 8 HOH A 10 610 51 HOH HOH . 
N 8 HOH A 11 611 22 HOH HOH . 
N 8 HOH A 12 612 20 HOH HOH . 
N 8 HOH A 13 613 14 HOH HOH . 
N 8 HOH A 14 614 43 HOH HOH . 
N 8 HOH A 15 615 47 HOH HOH . 
N 8 HOH A 16 616 40 HOH HOH . 
N 8 HOH A 17 617 25 HOH HOH . 
N 8 HOH A 18 618 48 HOH HOH . 
N 8 HOH A 19 619 53 HOH HOH . 
N 8 HOH A 20 620 54 HOH HOH . 
N 8 HOH A 21 621 33 HOH HOH . 
N 8 HOH A 22 622 1 HOH HOH . 
N 8 HOH A 23 623 35 HOH HOH . 
N 8 HOH A 24 624 49 HOH HOH . 
N 8 HOH A 25 625 9 HOH HOH . 
N 8 HOH A 26 626 38 HOH HOH . 
N 8 HOH A 27 627 13 HOH HOH . 
O 8 HOH B 1 601 28 HOH HOH . 
O 8 HOH B 2 602 21 HOH HOH . 
O 8 HOH B 3 603 2 HOH HOH . 
O 8 HOH B 4 604 39 HOH HOH . 
O 8 HOH B 5 605 3 HOH HOH . 
O 8 HOH B 6 606 44 HOH HOH . 
O 8 HOH B 7 607 5 HOH HOH . 
O 8 HOH B 8 608 4 HOH HOH . 
O 8 HOH B 9 609 50 HOH HOH . 
O 8 HOH B 10 610 24 HOH HOH . 
O 8 HOH B 11 611 46 HOH HOH . 
O 8 HOH B 12 612 15 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 O O1 OSB . . . M 5 40.433 -129.826 13.425 1 110.59 ? O1 OSB 505 B 1 
HETATM 2 O O2 OSB . . . M 5 40.91 -128.926 11.504 1 104.31 ? O2 OSB 505 B 1 
HETATM 3 C C7 OSB . . . M 5 40.265 -128.912 12.58 1 108.48 ? C7 OSB 505 B 1 
HETATM 4 C C6 OSB . . . M 5 38.581 -126.001 14.262 1 113.53 ? C6 OSB 505 B 1 
HETATM 5 C C5 OSB . . . M 5 37.515 -125.762 13.376 1 114.93 ? C5 OSB 505 B 1 
HETATM 6 C C4 OSB . . . M 5 37.359 -126.56 12.234 1 115.29 ? C4 OSB 505 B 1 
HETATM 7 C C3 OSB . . . M 5 38.251 -127.58 11.978 1 112.24 ? C3 OSB 505 B 1 
HETATM 8 C C2 OSB . . . M 5 39.307 -127.817 12.855 1 111.37 ? C2 OSB 505 B 1 
HETATM 9 C C1 OSB . . . M 5 39.465 -127.011 14.009 1 112.41 ? C1 OSB 505 B 1 
HETATM 10 C C8 OSB . . . M 5 40.625 -127.272 14.973 1 111.52 ? C8 OSB 505 B 1 
HETATM 11 C C9 OSB . . . M 5 40.41 -127.14 16.5 1 120.45 ? C9 OSB 505 B 1 
HETATM 12 O O3 OSB . . . M 5 41.721 -127.585 14.536 1 109.98 ? O3 OSB 505 B 1 
HETATM 13 C C10 OSB . . . M 5 41.708 -126.702 17.157 1 117.94 ? C10 OSB 505 B 1 
HETATM 14 C C11 OSB . . . M 5 41.398 -125.853 18.369 1 119.02 ? C11 OSB 505 B 1 
HETATM 15 O O4 OSB . . . M 5 42.229 -124.749 18.695 1 122.21 ? O4 OSB 505 B 1 
HETATM 16 O O5 OSB . . . M 5 40.436 -126.115 19.064 1 120.19 ? O5 OSB 505 B 1 
#
_model_server_stats.io_time_ms              74 
_model_server_stats.parse_time_ms           19 
_model_server_stats.create_model_time_ms    10 
_model_server_stats.query_time_ms           263 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           16 
#