data_5SVM
#
_model_server_result.job_id            rrIi2lPct8x0SBYQwu26Gw 
_model_server_result.datetime_utc      '2024-11-05 21:13:58' 
_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          5svm 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"O","auth_seq_id":406}' 
#
_entry.id    5SVM 
#
_exptl.entry_id    5SVM 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              62.068 
_entity.id                          6 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            1,2-ETHANEDIOL 
_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            5SVM 
_cell.length_a            172.64 
_cell.length_b            172.64 
_cell.length_c            172.64 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5SVM 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        198 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 21 3' 
#
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 trimeric 3 author_and_software_defined_assembly 1 
PISA trimeric 3 author_and_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,C,D,E,F,G,H,I,P 1 1,2,4 
B,J,K,L,M,N,O,Q 2 1,3,5 
#
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' 5_555 z,x,y 0 0 1 1 0 0 0 1 0 0 0 0 
3 'crystal symmetry operation' 6_555 z+1/2,-x+1/2,-y 0 0 1 -1 0 0 0 -1 0 86.32 86.32 0 
4 'crystal symmetry operation' 9_555 y,z,x 0 1 0 0 0 1 1 0 0 0 0 0 
5 'crystal symmetry operation' 12_554 -y+1/2,-z,x-1/2 0 -1 0 0 0 -1 1 0 0 86.32 0 -86.32 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 6 I N N 
? 6 O 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
disulf ? disulf1 A SG CYS 106 A CYS 107 1_555 A SG CYS 152 A CYS 153 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
disulf ? disulf2 A SG CYS 115 A CYS 116 1_555 A SG CYS 136 A CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
disulf ? disulf3 A SG CYS 121 A CYS 122 1_555 A SG CYS 146 A CYS 147 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf4 A SG CYS 202 A CYS 203 1_555 A SG CYS 212 A CYS 213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf5 A SG CYS 246 A CYS 247 1_555 A SG CYS 255 A CYS 256 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf6 B SG CYS 106 B CYS 107 1_555 B SG CYS 152 B CYS 153 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
disulf ? disulf7 B SG CYS 115 B CYS 116 1_555 B SG CYS 136 B CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf8 B SG CYS 121 B CYS 122 1_555 B SG CYS 146 B CYS 147 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf9 B SG CYS 202 B CYS 203 1_555 B SG CYS 212 B CYS 213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? 
disulf ? disulf10 B SG CYS 246 B CYS 247 1_555 B SG CYS 255 B CYS 256 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
covale ? covale1 A ND2 ASN 169 A ASN 170 1_555 C C1 NAG . A NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? 
covale ? covale2 A ND2 ASN 193 A ASN 194 1_555 D C1 NAG . A NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? 
covale ? covale3 A ND2 ASN 289 A ASN 290 1_555 E C1 NAG . A NAG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? 
covale ? covale4 B ND2 ASN 169 B ASN 170 1_555 K C1 NAG . B NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? 
covale ? covale5 B ND2 ASN 193 B ASN 194 1_555 L C1 NAG . B NAG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? 
covale ? covale6 B ND2 ASN 289 B ASN 290 1_555 M C1 NAG . B NAG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? 
metalc ? metalc1 F OAI 6AT . A 6AT 404 1_555 G NA NA . A NA 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.56 ? 
metalc ? metalc2 F OAC 6AT . A 6AT 404 1_555 G NA NA . A NA 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.011 ? 
metalc ? metalc3 G NA NA . A NA 405 1_555 P O HOH . A HOH 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.884 ? 
metalc ? metalc4 G NA NA . A NA 405 1_555 P O HOH . A HOH 511 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.65 ? 
metalc ? metalc5 G NA NA . A NA 405 1_555 P O HOH . A HOH 514 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.485 ? 
metalc ? metalc6 G NA NA . A NA 405 1_555 P O HOH . A HOH 518 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.334 ? 
metalc ? metalc7 B OD2 ASP 157 B ASP 158 1_555 N NA NA . B NA 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.705 ? 
metalc ? metalc8 N NA NA . B NA 405 1_555 Q O HOH . B HOH 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.002 ? 
metalc ? metalc9 N NA NA . B NA 405 1_555 Q O HOH . B HOH 512 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.961 ? 
#
_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 185 n n 
C1 C2 EDO sing 186 n n 
C1 H11 EDO sing 187 n n 
C1 H12 EDO sing 188 n n 
O1 HO1 EDO sing 189 n n 
C2 O2 EDO sing 190 n n 
C2 H21 EDO sing 191 n n 
C2 H22 EDO sing 192 n n 
O2 HO2 EDO sing 193 n n 
#
_atom_sites.entry_id                     5SVM 
_atom_sites.fract_transf_matrix[1][1]    0.005792 
_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]    0.005792 
_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]    0.005792 
_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 NAG A 1 401 500 NAG NAG . 
D 2 NAG A 1 402 501 NAG NAG . 
E 2 NAG A 1 403 502 NAG NAG . 
F 3 6AT A 1 404 1 6AT LIG . 
G 4 NA A 1 405 4 NA NA . 
H 5 TRS A 1 406 1 TRS TRS . 
I 6 EDO A 1 407 1 EDO EDO . 
J 7 ATP B 1 401 402 ATP ATP . 
K 2 NAG B 1 402 500 NAG NAG . 
L 2 NAG B 1 403 501 NAG NAG . 
M 2 NAG B 1 404 502 NAG NAG . 
N 4 NA B 1 405 3 NA NA . 
O 6 EDO B 1 406 2 EDO EDO . 
P 8 HOH A 1 501 20 HOH HOH . 
P 8 HOH A 2 502 40 HOH HOH . 
P 8 HOH A 3 503 52 HOH HOH . 
P 8 HOH A 4 504 3 HOH HOH . 
P 8 HOH A 5 505 44 HOH HOH . 
P 8 HOH A 6 506 6 HOH HOH . 
P 8 HOH A 7 507 1 HOH HOH . 
P 8 HOH A 8 508 5 HOH HOH . 
P 8 HOH A 9 509 4 HOH HOH . 
P 8 HOH A 10 510 11 HOH HOH . 
P 8 HOH A 11 511 43 HOH HOH . 
P 8 HOH A 12 512 14 HOH HOH . 
P 8 HOH A 13 513 26 HOH HOH . 
P 8 HOH A 14 514 49 HOH HOH . 
P 8 HOH A 15 515 54 HOH HOH . 
P 8 HOH A 16 516 15 HOH HOH . 
P 8 HOH A 17 517 45 HOH HOH . 
P 8 HOH A 18 518 42 HOH HOH . 
P 8 HOH A 19 519 2 HOH HOH . 
Q 8 HOH B 1 501 29 HOH HOH . 
Q 8 HOH B 2 502 22 HOH HOH . 
Q 8 HOH B 3 503 48 HOH HOH . 
Q 8 HOH B 4 504 37 HOH HOH . 
Q 8 HOH B 5 505 36 HOH HOH . 
Q 8 HOH B 6 506 23 HOH HOH . 
Q 8 HOH B 7 507 33 HOH HOH . 
Q 8 HOH B 8 508 51 HOH HOH . 
Q 8 HOH B 9 509 19 HOH HOH . 
Q 8 HOH B 10 510 50 HOH HOH . 
Q 8 HOH B 11 511 28 HOH HOH . 
Q 8 HOH B 12 512 32 HOH HOH . 
Q 8 HOH B 13 513 16 HOH HOH . 
Q 8 HOH B 14 514 35 HOH HOH . 
Q 8 HOH B 15 515 53 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 . . . O 6 42.983 29.238 -20.128 1 67.29 ? C1 EDO 406 B 1 
HETATM 2 O O1 EDO . . . O 6 41.603 29.639 -20.111 1 84.91 ? O1 EDO 406 B 1 
HETATM 3 C C2 EDO . . . O 6 43.854 30.522 -19.921 1 80.84 ? C2 EDO 406 B 1 
HETATM 4 O O2 EDO . . . O 6 44.631 30.72 -21.069 1 91.61 ? O2 EDO 406 B 1 
HETATM 5 H H11 EDO . . . O 6 43.2 28.824 -21.002 1 80.74 ? H11 EDO 406 B 1 
HETATM 6 H H12 EDO . . . O 6 43.149 28.613 -19.423 1 80.74 ? H12 EDO 406 B 1 
HETATM 7 H HO1 EDO . . . O 6 41.075 28.908 -19.947 1 101.9 ? HO1 EDO 406 B 1 
HETATM 8 H H21 EDO . . . O 6 44.457 30.396 -19.124 1 97 ? H21 EDO 406 B 1 
HETATM 9 H H22 EDO . . . O 6 43.276 31.291 -19.781 1 97 ? H22 EDO 406 B 1 
HETATM 10 H HO2 EDO . . . O 6 45.371 31.138 -20.849 1 109.93 ? HO2 EDO 406 B 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    11 
_model_server_stats.query_time_ms           230 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           10 
#