data_5SVK
#
_model_server_result.job_id            3DBvkdOK-uVMwsLkn0PIZw 
_model_server_result.datetime_utc      '2024-11-26 21:16:11' 
_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          5svk 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"L","auth_seq_id":408}' 
#
_entry.id    5SVK 
#
_exptl.entry_id    5SVK 
_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    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            5SVK 
_cell.length_a            173.15 
_cell.length_b            173.15 
_cell.length_c            173.15 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5SVK 
_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,G,H,I,J,K,L,M,S 1 1,2,4 
B,E,F,N,O,P,Q,R,T 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_577 z+1/2,-x+5/2,-y+2 0 0 1 -1 0 0 0 -1 0 86.575 432.875 346.3 
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_774 -y+5/2,-z+2,x-1/2 0 -1 0 0 0 -1 1 0 0 432.875 346.3 -86.575 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 5 L N N 
? 5 R N N 
#
_pdbx_entity_branch.entity_id    2 
_pdbx_entity_branch.type         oligosaccharide 
#
_pdbx_entity_branch_link.link_id                     1 
_pdbx_entity_branch_link.details                     ? 
_pdbx_entity_branch_link.entity_id                   2 
_pdbx_entity_branch_link.entity_branch_list_num_1    2 
_pdbx_entity_branch_link.entity_branch_list_num_2    1 
_pdbx_entity_branch_link.comp_id_1                   GLC 
_pdbx_entity_branch_link.comp_id_2                   GLC 
_pdbx_entity_branch_link.atom_id_1                   C1 
_pdbx_entity_branch_link.leaving_atom_id_1           O1 
_pdbx_entity_branch_link.atom_stereo_config_1        . 
_pdbx_entity_branch_link.atom_id_2                   O4 
_pdbx_entity_branch_link.leaving_atom_id_2           HO4 
_pdbx_entity_branch_link.atom_stereo_config_2        . 
_pdbx_entity_branch_link.value_order                 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 C GLC 1 C 1 GLC A 504 MAL 
2 n C GLC 2 C 2 GLC A 504 MAL 
2 n D GLC 1 D 1 GLC J 2 MAL 
2 n D GLC 2 D 2 GLC J 2 MAL 
2 n E GLC 1 E 1 GLC B 503 MAL 
2 n E GLC 2 E 2 GLC B 503 MAL 
2 n F GLC 1 F 1 GLC J 1 MAL 
2 n F GLC 2 F 2 GLC J 1 MAL 
#
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 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? 
disulf ? disulf2 A SG CYS 115 A CYS 116 1_555 A SG CYS 136 A CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf3 A SG CYS 121 A CYS 122 1_555 A SG CYS 146 A CYS 147 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
disulf ? disulf4 A SG CYS 202 A CYS 203 1_555 A SG CYS 212 A CYS 213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? 
disulf ? disulf5 A SG CYS 246 A CYS 247 1_555 A SG CYS 255 A CYS 256 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf6 B SG CYS 106 B CYS 107 1_555 B SG CYS 152 B CYS 153 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? 
disulf ? disulf7 B SG CYS 115 B CYS 116 1_555 B SG CYS 136 B CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
disulf ? disulf8 B SG CYS 121 B CYS 122 1_555 B SG CYS 146 B CYS 147 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
disulf ? disulf9 B SG CYS 202 B CYS 203 1_555 B SG CYS 212 B CYS 213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? 
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 138 A ASN 139 1_555 K C1 NAG . A NAG 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? 
covale ? covale2 A ND2 ASN 169 A ASN 170 1_555 H C1 NAG . A NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? 
covale ? covale3 A ND2 ASN 193 A ASN 194 1_555 I C1 NAG . A NAG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? 
covale ? covale4 A ND2 ASN 289 A ASN 290 1_555 J C1 NAG . A NAG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? 
covale ? covale5 B ND2 ASN 169 B ASN 170 1_555 O C1 NAG . B NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? 
covale ? covale6 B ND2 ASN 193 B ASN 194 1_555 P C1 NAG . B NAG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? 
covale ? covale7 B ND2 ASN 289 B ASN 290 1_555 Q C1 NAG . B NAG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? 
covale ? covale8 C O4 GLC . C GLC 1 1_555 C C1 GLC . C GLC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.411 sing 
covale ? covale9 D O4 GLC . D GLC 1 1_555 D C1 GLC . D GLC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.413 sing 
covale ? covale10 E O4 GLC . E GLC 1 1_555 E C1 GLC . E GLC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.412 sing 
covale ? covale11 F O4 GLC . F GLC 1 1_555 F C1 GLC . F GLC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.414 sing 
#
_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 132 n n 
C1 C2 EDO sing 133 n n 
C1 H11 EDO sing 134 n n 
C1 H12 EDO sing 135 n n 
O1 HO1 EDO sing 136 n n 
C2 O2 EDO sing 137 n n 
C2 H21 EDO sing 138 n n 
C2 H22 EDO sing 139 n n 
O2 HO2 EDO sing 140 n n 
#
_atom_sites.entry_id                     5SVK 
_atom_sites.fract_transf_matrix[1][1]    0.005775 
_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]    0.005775 
_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]    0.005775 
_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
G 3 ATP A 1 401 402 ATP ATP . 
H 4 NAG A 1 402 500 NAG NAG . 
I 4 NAG A 1 403 501 NAG NAG . 
J 4 NAG A 1 404 502 NAG NAG . 
K 4 NAG A 1 405 503 NAG NAG . 
L 5 EDO A 1 408 1 EDO EDO . 
M 6 MHA A 1 409 1 MHA LIG . 
N 3 ATP B 1 401 402 ATP ATP . 
O 4 NAG B 1 402 500 NAG NAG . 
P 4 NAG B 1 403 501 NAG NAG . 
Q 4 NAG B 1 404 502 NAG NAG . 
R 5 EDO B 1 407 2 EDO EDO . 
S 7 HOH A 1 501 33 HOH HOH . 
S 7 HOH A 2 502 60 HOH HOH . 
S 7 HOH A 3 503 23 HOH HOH . 
S 7 HOH A 4 504 22 HOH HOH . 
S 7 HOH A 5 505 8 HOH HOH . 
S 7 HOH A 6 506 1 HOH HOH . 
S 7 HOH A 7 507 55 HOH HOH . 
S 7 HOH A 8 508 4 HOH HOH . 
S 7 HOH A 9 509 81 HOH HOH . 
S 7 HOH A 10 510 64 HOH HOH . 
S 7 HOH A 11 511 12 HOH HOH . 
S 7 HOH A 12 512 27 HOH HOH . 
S 7 HOH A 13 513 34 HOH HOH . 
S 7 HOH A 14 514 17 HOH HOH . 
S 7 HOH A 15 515 53 HOH HOH . 
S 7 HOH A 16 516 14 HOH HOH . 
S 7 HOH A 17 517 68 HOH HOH . 
S 7 HOH A 18 518 5 HOH HOH . 
S 7 HOH A 19 519 13 HOH HOH . 
S 7 HOH A 20 520 16 HOH HOH . 
S 7 HOH A 21 521 56 HOH HOH . 
S 7 HOH A 22 522 28 HOH HOH . 
S 7 HOH A 23 523 26 HOH HOH . 
S 7 HOH A 24 524 31 HOH HOH . 
S 7 HOH A 25 525 9 HOH HOH . 
S 7 HOH A 26 526 80 HOH HOH . 
S 7 HOH A 27 527 3 HOH HOH . 
S 7 HOH A 28 528 32 HOH HOH . 
S 7 HOH A 29 529 20 HOH HOH . 
S 7 HOH A 30 530 6 HOH HOH . 
S 7 HOH A 31 531 57 HOH HOH . 
S 7 HOH A 32 532 10 HOH HOH . 
S 7 HOH A 33 533 62 HOH HOH . 
S 7 HOH A 34 534 7 HOH HOH . 
S 7 HOH A 35 535 71 HOH HOH . 
S 7 HOH A 36 536 19 HOH HOH . 
S 7 HOH A 37 537 70 HOH HOH . 
S 7 HOH A 38 538 54 HOH HOH . 
S 7 HOH A 39 539 11 HOH HOH . 
T 7 HOH B 1 501 66 HOH HOH . 
T 7 HOH B 2 502 75 HOH HOH . 
T 7 HOH B 3 503 36 HOH HOH . 
T 7 HOH B 4 504 47 HOH HOH . 
T 7 HOH B 5 505 45 HOH HOH . 
T 7 HOH B 6 506 42 HOH HOH . 
T 7 HOH B 7 507 82 HOH HOH . 
T 7 HOH B 8 508 46 HOH HOH . 
T 7 HOH B 9 509 41 HOH HOH . 
T 7 HOH B 10 510 39 HOH HOH . 
T 7 HOH B 11 511 61 HOH HOH . 
T 7 HOH B 12 512 63 HOH HOH . 
T 7 HOH B 13 513 49 HOH HOH . 
T 7 HOH B 14 514 67 HOH HOH . 
T 7 HOH B 15 515 74 HOH HOH . 
T 7 HOH B 16 516 59 HOH HOH . 
T 7 HOH B 17 517 48 HOH HOH . 
T 7 HOH B 18 518 77 HOH HOH . 
T 7 HOH B 19 519 43 HOH HOH . 
T 7 HOH B 20 520 65 HOH HOH . 
T 7 HOH B 21 521 69 HOH HOH . 
T 7 HOH B 22 522 72 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 5 186.105 171.553 181.061 1 95.86 ? C1 EDO 408 A 1 
HETATM 2 O O1 EDO . . . L 5 185.484 172.404 180.089 1 99.36 ? O1 EDO 408 A 1 
HETATM 3 C C2 EDO . . . L 5 186.881 170.449 180.349 1 112.17 ? C2 EDO 408 A 1 
HETATM 4 O O2 EDO . . . L 5 187.44 169.558 181.321 1 110.97 ? O2 EDO 408 A 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    8 
_model_server_stats.query_time_ms           318 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           4 
#