data_6V3U
#
_model_server_result.job_id            YOmDkyFYQQKk0K-6gBoDaQ 
_model_server_result.datetime_utc      '2024-11-15 09:35:28' 
_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          6v3u 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"L","auth_seq_id":305}' 
#
_entry.id    6V3U 
#
_exptl.entry_id    6V3U 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              62.068 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            1,2-ETHANEDIOL 
_entity.pdbx_number_of_molecules    4 
_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            6V3U 
_cell.length_a            80.043 
_cell.length_b            80.043 
_cell.length_c            72.502 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6V3U 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        76 
_symmetry.space_group_name_Hall    'P 4w' 
_symmetry.space_group_name_H-M     'P 41' 
#
_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 
_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 F N N 
? 5 J N N 
? 5 K N N 
? 5 L 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 A C TRP 32 A TRP 51 1_555 A N MSE 33 A MSE 52 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? 
covale ? covale2 A C MSE 33 A MSE 52 1_555 A N HIS 34 A HIS 53 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? 
covale ? covale3 A C LEU 40 A LEU 59 1_555 A N MSE 41 A MSE 60 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? 
covale ? covale4 A C MSE 41 A MSE 60 1_555 A N GLY 42 A GLY 61 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? 
covale ? covale5 A C SER 79 A SER 98 1_555 A N MSE 80 A MSE 99 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? 
covale ? covale6 A C MSE 80 A MSE 99 1_555 A N VAL 81 A VAL 100 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? 
covale ? covale7 A C LYS 98 A LYS 117 1_555 A N MSE 99 A MSE 118 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? 
covale ? covale8 A C MSE 99 A MSE 118 1_555 A N GLY 100 A GLY 119 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 ? 
covale ? covale9 A C GLY 101 A GLY 120 1_555 A N MSE 102 A MSE 121 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? 
covale ? covale10 A C MSE 102 A MSE 121 1_555 A N ALA 103 A ALA 122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? 
covale ? covale11 A C GLY 180 A GLY 199 1_555 A N OCS 181 A OCS 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? 
covale ? covale12 A C OCS 181 A OCS 200 1_555 A N MSE 182 A MSE 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? 
covale ? covale13 A C MSE 182 A MSE 201 1_555 A N ILE 183 A ILE 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.34 ? 
covale ? covale14 A C ALA 220 A ALA 239 1_555 A N MSE 221 A MSE 240 1_555 ? ? ? ? A ? ? ? ? ? ? ? 1.325 ? 
covale ? covale15 A C ALA 220 A ALA 239 1_555 A N MSE 221 A MSE 240 1_555 ? ? ? ? B ? ? ? ? ? ? ? 1.328 ? 
covale ? covale16 A C MSE 221 A MSE 240 1_555 A N SER 222 A SER 241 1_555 ? A ? ? ? ? ? ? ? ? ? ? 1.335 ? 
covale ? covale17 A C MSE 221 A MSE 240 1_555 A N SER 222 A SER 241 1_555 ? B ? ? ? ? ? ? ? ? ? ? 1.336 ? 
covale ? covale18 B C TRP 32 B TRP 51 1_555 B N MSE 33 B MSE 52 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? 
covale ? covale19 B C MSE 33 B MSE 52 1_555 B N HIS 34 B HIS 53 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? 
covale ? covale20 B C LEU 40 B LEU 59 1_555 B N MSE 41 B MSE 60 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? 
covale ? covale21 B C MSE 41 B MSE 60 1_555 B N GLY 42 B GLY 61 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? 
covale ? covale22 B C SER 79 B SER 98 1_555 B N MSE 80 B MSE 99 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? 
covale ? covale23 B C MSE 80 B MSE 99 1_555 B N VAL 81 B VAL 100 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? 
covale ? covale24 B C LYS 98 B LYS 117 1_555 B N MSE 99 B MSE 118 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? 
covale ? covale25 B C MSE 99 B MSE 118 1_555 B N GLY 100 B GLY 119 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? 
covale ? covale26 B C GLY 101 B GLY 120 1_555 B N MSE 102 B MSE 121 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? 
covale ? covale27 B C MSE 102 B MSE 121 1_555 B N ALA 103 B ALA 122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? 
covale ? covale28 B C GLY 180 B GLY 199 1_555 B N OCS 181 B OCS 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? 
covale ? covale29 B C OCS 181 B OCS 200 1_555 B N MSE 182 B MSE 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? 
covale ? covale30 B C MSE 182 B MSE 201 1_555 B N ILE 183 B ILE 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? 
covale ? covale31 B C ALA 220 B ALA 239 1_555 B N MSE 221 B MSE 240 1_555 ? ? ? ? A ? ? ? ? ? ? ? 1.327 ? 
covale ? covale32 B C ALA 220 B ALA 239 1_555 B N MSE 221 B MSE 240 1_555 ? ? ? ? B ? ? ? ? ? ? ? 1.333 ? 
covale ? covale33 B C MSE 221 B MSE 240 1_555 B N SER 222 B SER 241 1_555 ? A ? ? ? ? ? ? ? ? ? ? 1.333 ? 
covale ? covale34 B C MSE 221 B MSE 240 1_555 B N SER 222 B SER 241 1_555 ? B ? ? ? ? ? ? ? ? ? ? 1.336 ? 
metalc ? metalc1 A ND1 HIS 93 A HIS 112 1_555 C ZN ZN . A ZN 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.993 ? 
metalc ? metalc2 A NE2 HIS 95 A HIS 114 1_555 C ZN ZN . A ZN 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.976 ? 
metalc ? metalc3 A OD1 ASP 196 A ASP 215 1_555 G ZN ZN . B ZN 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? 
metalc ? metalc4 A NE2 HIS 223 A HIS 242 1_555 C ZN ZN . A ZN 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.81 ? 
metalc ? metalc5 C ZN ZN . A ZN 300 1_555 B OD1 ASP 196 B ASP 215 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.987 ? 
metalc ? metalc6 B ND1 HIS 93 B HIS 112 1_555 G ZN ZN . B ZN 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.989 ? 
metalc ? metalc7 B NE2 HIS 95 B HIS 114 1_555 G ZN ZN . B ZN 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? 
metalc ? metalc8 B NE2 HIS 223 B HIS 242 1_555 G ZN ZN . B ZN 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.781 ? 
#
_chem_comp.formula           'C2 H6 O2' 
_chem_comp.formula_weight    62.068 
_chem_comp.id                EDO 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              1,2-ETHANEDIOL 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     'ETHYLENE GLYCOL' 
#
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 EDO sing 70 n n 
C1 C2 EDO sing 71 n n 
C1 H11 EDO sing 72 n n 
C1 H12 EDO sing 73 n n 
O1 HO1 EDO sing 74 n n 
C2 O2 EDO sing 75 n n 
C2 H21 EDO sing 76 n n 
C2 H22 EDO sing 77 n n 
O2 HO2 EDO sing 78 n n 
#
_atom_sites.entry_id                     6V3U 
_atom_sites.fract_transf_matrix[1][1]    0.012493 
_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]    0.012493 
_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]    0.013793 
_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 ZN A 1 300 300 ZN ZN . 
D 3 SO4 A 1 301 301 SO4 SO4 . 
E 4 IPA A 1 302 302 IPA IPA . 
F 5 EDO A 1 303 303 EDO EDO . 
G 2 ZN B 1 300 300 ZN ZN . 
H 3 SO4 B 1 301 301 SO4 SO4 . 
I 4 IPA B 1 302 302 IPA IPA . 
J 5 EDO B 1 303 303 EDO EDO . 
K 5 EDO B 1 304 304 EDO EDO . 
L 5 EDO B 1 305 305 EDO EDO . 
M 6 HOH A 1 401 1 HOH HOH . 
M 6 HOH A 2 402 26 HOH HOH . 
M 6 HOH A 3 403 4 HOH HOH . 
M 6 HOH A 4 404 8 HOH HOH . 
M 6 HOH A 5 405 7 HOH HOH . 
M 6 HOH A 6 406 9 HOH HOH . 
M 6 HOH A 7 407 11 HOH HOH . 
M 6 HOH A 8 408 14 HOH HOH . 
M 6 HOH A 9 409 19 HOH HOH . 
M 6 HOH A 10 410 3 HOH HOH . 
M 6 HOH A 11 411 13 HOH HOH . 
M 6 HOH A 12 412 15 HOH HOH . 
M 6 HOH A 13 413 18 HOH HOH . 
M 6 HOH A 14 414 23 HOH HOH . 
M 6 HOH A 15 415 16 HOH HOH . 
M 6 HOH A 16 416 24 HOH HOH . 
M 6 HOH A 17 417 2 HOH HOH . 
M 6 HOH A 18 418 21 HOH HOH . 
M 6 HOH A 19 419 17 HOH HOH . 
M 6 HOH A 20 420 6 HOH HOH . 
M 6 HOH A 21 421 22 HOH HOH . 
M 6 HOH A 22 422 5 HOH HOH . 
M 6 HOH A 23 423 25 HOH HOH . 
M 6 HOH A 24 424 10 HOH HOH . 
M 6 HOH A 25 425 12 HOH HOH . 
N 6 HOH B 1 401 38 HOH HOH . 
N 6 HOH B 2 402 54 HOH HOH . 
N 6 HOH B 3 403 44 HOH HOH . 
N 6 HOH B 4 404 45 HOH HOH . 
N 6 HOH B 5 405 46 HOH HOH . 
N 6 HOH B 6 406 37 HOH HOH . 
N 6 HOH B 7 407 51 HOH HOH . 
N 6 HOH B 8 408 41 HOH HOH . 
N 6 HOH B 9 409 31 HOH HOH . 
N 6 HOH B 10 410 48 HOH HOH . 
N 6 HOH B 11 411 29 HOH HOH . 
N 6 HOH B 12 412 27 HOH HOH . 
N 6 HOH B 13 413 34 HOH HOH . 
N 6 HOH B 14 414 30 HOH HOH . 
N 6 HOH B 15 415 43 HOH HOH . 
N 6 HOH B 16 416 35 HOH HOH . 
N 6 HOH B 17 417 40 HOH HOH . 
N 6 HOH B 18 418 56 HOH HOH . 
N 6 HOH B 19 419 28 HOH HOH . 
N 6 HOH B 20 420 49 HOH HOH . 
N 6 HOH B 21 421 42 HOH HOH . 
N 6 HOH B 22 422 55 HOH HOH . 
N 6 HOH B 23 423 47 HOH HOH . 
N 6 HOH B 24 424 33 HOH HOH . 
N 6 HOH B 25 425 32 HOH HOH . 
N 6 HOH B 26 426 39 HOH HOH . 
N 6 HOH B 27 427 57 HOH HOH . 
N 6 HOH B 28 428 20 HOH HOH . 
N 6 HOH B 29 429 50 HOH HOH . 
N 6 HOH B 30 430 52 HOH HOH . 
N 6 HOH B 31 431 53 HOH HOH . 
N 6 HOH B 32 432 36 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 EDO . . . L 5 38.929 0.151 36.826 1 99.43 ? C1 EDO 305 B 1 
HETATM 2 O O1 EDO . . . L 5 38.435 0.067 35.486 1 100.97 ? O1 EDO 305 B 1 
HETATM 3 C C2 EDO . . . L 5 39.862 -1.026 37.091 1 96.95 ? C2 EDO 305 B 1 
HETATM 4 O O2 EDO . . . L 5 40.878 -1.055 36.078 1 90.88 ? O2 EDO 305 B 1 
#
_model_server_stats.io_time_ms              18 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           315 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           4 
#