data_3KVB
#
_model_server_result.job_id            Grc-C1rJ9Rch9UxYtFXdIQ 
_model_server_result.datetime_utc      '2024-12-03 14:53:52' 
_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          3kvb 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":5798}' 
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_entry.id    3KVB 
#
_exptl.entry_id    3KVB 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              147.086 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            N-OXALYLGLYCINE 
_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            3KVB 
_cell.length_a            78.3 
_cell.length_b            78.3 
_cell.length_c            289.1 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
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_symmetry.entry_id                 3KVB 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        178 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 61 2 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
? monomeric 1 author_defined_assembly 1 
PISA dimeric 2 software_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 
A,B,C,D,E,F 2 1,2 
#
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' 12_565 x,x-y+1,-z+1/6 0.5 0.866025 0 0.866025 -0.5 0 0 0 -1 -39.15 67.809789 48.183333 
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_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 
#
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 NE2 HIS 191 A HIS 282 1_555 B NI NI . A NI 489 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.482 ? 
metalc ? metalc2 A OD1 ASP 193 A ASP 284 1_555 B NI NI . A NI 489 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.371 ? 
metalc ? metalc3 A NE2 HIS 263 A HIS 354 1_555 B NI NI . A NI 489 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.364 ? 
metalc ? metalc4 B NI NI . A NI 489 1_555 E O2' OGA . A OGA 5798 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.927 ? 
metalc ? metalc5 B NI NI . A NI 489 1_555 E O2 OGA . A OGA 5798 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? 
#
_chem_comp.formula           'C4 H5 N O5' 
_chem_comp.formula_weight    147.086 
_chem_comp.id                OGA 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              N-OXALYLGLYCINE 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ? 
#
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 C2 OGA sing 237 n n 
C1 O1 OGA doub 238 n n 
C1 O2 OGA sing 239 n n 
C2 O2' OGA doub 240 n n 
C2 N1 OGA sing 241 n n 
C4 C5 OGA sing 242 n n 
C4 N1 OGA sing 243 n n 
C4 H4C1 OGA sing 244 n n 
C4 H4C2 OGA sing 245 n n 
C5 O3 OGA sing 246 n n 
C5 O4 OGA doub 247 n n 
O2 H2 OGA sing 248 n n 
O3 H3 OGA sing 249 n n 
N1 H1 OGA sing 250 n n 
#
_atom_sites.entry_id                     3KVB 
_atom_sites.fract_transf_matrix[1][1]    0.012771 
_atom_sites.fract_transf_matrix[1][2]    0.007374 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.014747 
_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]    0.003459 
_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 1 489 480 NI NI . 
C 2 NI A 1 490 481 NI NI . 
D 3 OXY A 1 491 482 OXY OXY . 
E 4 OGA A 1 5798 5798 OGA OGA . 
F 5 HOH A 1 1 1 HOH TIP . 
F 5 HOH A 2 2 2 HOH TIP . 
F 5 HOH A 3 3 3 HOH TIP . 
F 5 HOH A 4 4 4 HOH TIP . 
F 5 HOH A 5 5 5 HOH TIP . 
F 5 HOH A 6 6 6 HOH TIP . 
F 5 HOH A 7 7 7 HOH TIP . 
F 5 HOH A 8 8 8 HOH TIP . 
F 5 HOH A 9 9 9 HOH TIP . 
F 5 HOH A 10 10 10 HOH TIP . 
F 5 HOH A 11 11 11 HOH TIP . 
F 5 HOH A 12 12 12 HOH TIP . 
F 5 HOH A 13 13 13 HOH TIP . 
F 5 HOH A 14 14 14 HOH TIP . 
F 5 HOH A 15 15 15 HOH TIP . 
F 5 HOH A 16 16 16 HOH TIP . 
F 5 HOH A 17 17 17 HOH TIP . 
F 5 HOH A 18 18 18 HOH TIP . 
F 5 HOH A 19 19 19 HOH TIP . 
F 5 HOH A 20 20 20 HOH TIP . 
F 5 HOH A 21 21 21 HOH TIP . 
F 5 HOH A 22 22 22 HOH TIP . 
F 5 HOH A 23 23 23 HOH TIP . 
F 5 HOH A 24 24 24 HOH TIP . 
F 5 HOH A 25 25 25 HOH TIP . 
F 5 HOH A 26 26 26 HOH TIP . 
F 5 HOH A 27 27 27 HOH TIP . 
F 5 HOH A 28 28 28 HOH TIP . 
F 5 HOH A 29 29 29 HOH TIP . 
F 5 HOH A 30 30 30 HOH TIP . 
F 5 HOH A 31 31 31 HOH TIP . 
F 5 HOH A 32 33 33 HOH TIP . 
F 5 HOH A 33 34 34 HOH TIP . 
F 5 HOH A 34 35 35 HOH TIP . 
F 5 HOH A 35 36 36 HOH TIP . 
F 5 HOH A 36 38 38 HOH TIP . 
F 5 HOH A 37 39 39 HOH TIP . 
F 5 HOH A 38 40 40 HOH TIP . 
#
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 OGA . . . E 4 -41.754 23.525 10.239 1 105.2 ? C1 OGA 5798 A 1 
HETATM 2 C C2 OGA . . . E 4 -42.695 23.165 9.123 1 105.21 ? C2 OGA 5798 A 1 
HETATM 3 C C4 OGA . . . E 4 -43.867 21.317 7.877 1 104.67 ? C4 OGA 5798 A 1 
HETATM 4 C C5 OGA . . . E 4 -44.277 19.871 7.973 1 104.87 ? C5 OGA 5798 A 1 
HETATM 5 O O1 OGA . . . E 4 -41.303 22.693 10.997 1 105.2 ? O1 OGA 5798 A 1 
HETATM 6 O O2 OGA . . . E 4 -41.343 24.79 10.452 1 105.58 ? O2 OGA 5798 A 1 
HETATM 7 O O2' OGA . . . E 4 -43.097 24.044 8.375 1 104.24 ? O2' OGA 5798 A 1 
HETATM 8 O O3 OGA . . . E 4 -44.943 19.313 6.961 1 105.84 ? O3 OGA 5798 A 1 
HETATM 9 N N1 OGA . . . E 4 -43.06 21.867 8.973 1 104.65 ? N1 OGA 5798 A 1 
HETATM 10 O O4 OGA . . . E 4 -44.057 19.158 8.917 1 105.17 ? O4 OGA 5798 A 1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           328 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           10 
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