data_7KD0
#
_model_server_result.job_id            0NNRrHsre4HtxvX2EjWZ5w 
_model_server_result.datetime_utc      '2025-09-04 23:47:44' 
_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          7kd0 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":302}' 
#
_entry.id    7KD0 
#
_exptl.entry_id    7KD0 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              62.068 
_entity.id                          7 
_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            7KD0 
_cell.length_a            76.223 
_cell.length_b            100.817 
_cell.length_c            129.712 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7KD0 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    trimeric 
_pdbx_struct_assembly.oligomeric_count      3 
_pdbx_struct_assembly.details               author_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,P,Q,R,S,T 
_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
? 7 H N N 
? 7 I N N 
#
loop_
_pdbx_entity_branch.entity_id
_pdbx_entity_branch.type
4 oligosaccharide 
5 oligosaccharide 
#
loop_
_pdbx_entity_branch_link.link_id
_pdbx_entity_branch_link.details
_pdbx_entity_branch_link.entity_id
_pdbx_entity_branch_link.entity_branch_list_num_1
_pdbx_entity_branch_link.entity_branch_list_num_2
_pdbx_entity_branch_link.comp_id_1
_pdbx_entity_branch_link.comp_id_2
_pdbx_entity_branch_link.atom_id_1
_pdbx_entity_branch_link.leaving_atom_id_1
_pdbx_entity_branch_link.atom_stereo_config_1
_pdbx_entity_branch_link.atom_id_2
_pdbx_entity_branch_link.leaving_atom_id_2
_pdbx_entity_branch_link.atom_stereo_config_2
_pdbx_entity_branch_link.value_order
1 ? 4 2 1 FUC NAG C1 O1 . O3 HO3 . sing 
2 ? 4 3 1 NAG NAG C1 O1 . O4 HO4 . sing 
3 ? 5 2 1 NAG NAG C1 O1 . O4 HO4 . sing 
4 ? 5 3 2 BMA NAG C1 O1 . O4 HO4 . 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
4 n D NAG 1 D 1 NAG A 270 NDG 
4 n D FUC 2 D 2 FUC A 273 FUC 
4 n D NAG 3 D 3 NAG A 271 NAG 
5 n E NAG 1 E 1 NAG B 270 NDG 
5 n E NAG 2 E 2 NAG B 271 NAG 
5 n E BMA 3 E 3 BMA B 272 BMA 
5 n F NAG 1 F 1 NAG B 280 NDG 
5 n F NAG 2 F 2 NAG B 281 NAG 
5 n F BMA 3 F 3 BMA B 282 BMA 
#
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 259 A CYS 259 1_555 B SG CYS 4 B CYS 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? 
disulf ? disulf2 B SG CYS 20 B CYS 20 1_555 B SG CYS 39 B CYS 39 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf3 B SG CYS 63 B CYS 63 1_555 B SG CYS 80 B CYS 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf4 B SG CYS 151 B CYS 151 1_555 B SG CYS 164 B CYS 164 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? 
disulf ? disulf5 B SG CYS 190 B CYS 190 1_555 B SG CYS 207 B CYS 207 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? 
covale ? covale1 A ND2 ASN 10 A ASN 10 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? 
covale ? covale2 B ND2 ASN 95 B ASN 95 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? 
covale ? covale3 B ND2 ASN 135 B ASN 135 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? 
covale ? covale4 D O3 NAG . D NAG 1 1_555 D C1 FUC . D FUC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? 
covale ? covale5 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? 
covale ? covale6 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? 
covale ? covale7 E O4 NAG . E NAG 2 1_555 E C1 BMA . E BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? 
covale ? covale8 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? 
covale ? covale9 F O4 NAG . F NAG 2 1_555 F C1 BMA . F BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? 
metalc ? metalc1 A NE2 HIS 65 A HIS 65 1_555 J ZN ZN . A ZN 304 4_476 ? ? ? ? ? ? ? ? ? ? ? ? 2.197 ? 
metalc ? metalc2 A OE1 GLU 102 A GLU 102 1_555 J ZN ZN . A ZN 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.594 ? 
metalc ? metalc3 A OE2 GLU 102 A GLU 102 1_555 J ZN ZN . A ZN 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? 
metalc ? metalc4 A NE2 HIS 106 A HIS 106 1_555 J ZN ZN . A ZN 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.096 ? 
#
_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 107 n n 
C1 C2 EDO sing 108 n n 
C1 H11 EDO sing 109 n n 
C1 H12 EDO sing 110 n n 
O1 HO1 EDO sing 111 n n 
C2 O2 EDO sing 112 n n 
C2 H21 EDO sing 113 n n 
C2 H22 EDO sing 114 n n 
O2 HO2 EDO sing 115 n n 
#
_atom_sites.entry_id                     7KD0 
_atom_sites.fract_transf_matrix[1][1]    0.013119 
_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]    0.009919 
_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]    0.007709 
_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 6 GAL A 1 301 2 GAL GAL . 
H 7 EDO A 1 302 3 EDO EDO . 
I 7 EDO A 1 303 4 EDO EDO . 
J 8 ZN A 1 304 5 ZN ZN . 
K 9 CL A 1 305 6 CL CL . 
L 9 CL A 1 306 7 CL CL . 
M 9 CL A 1 307 9 CL CL . 
N 9 CL A 1 308 10 CL CL . 
O 9 CL A 1 309 11 CL CL . 
P 6 GAL B 1 301 1 GAL GAL . 
Q 9 CL B 1 302 8 CL CL . 
R 10 HOH A 1 401 19 HOH HOH . 
R 10 HOH A 2 402 7 HOH HOH . 
R 10 HOH A 3 403 131 HOH HOH . 
R 10 HOH A 4 404 149 HOH HOH . 
R 10 HOH A 5 405 142 HOH HOH . 
R 10 HOH A 6 406 96 HOH HOH . 
R 10 HOH A 7 407 88 HOH HOH . 
R 10 HOH A 8 408 74 HOH HOH . 
R 10 HOH A 9 409 31 HOH HOH . 
R 10 HOH A 10 410 54 HOH HOH . 
R 10 HOH A 11 411 102 HOH HOH . 
R 10 HOH A 12 412 40 HOH HOH . 
R 10 HOH A 13 413 13 HOH HOH . 
R 10 HOH A 14 414 27 HOH HOH . 
R 10 HOH A 15 415 42 HOH HOH . 
R 10 HOH A 16 416 67 HOH HOH . 
R 10 HOH A 17 417 55 HOH HOH . 
R 10 HOH A 18 418 32 HOH HOH . 
R 10 HOH A 19 419 8 HOH HOH . 
R 10 HOH A 20 420 48 HOH HOH . 
R 10 HOH A 21 421 59 HOH HOH . 
R 10 HOH A 22 422 146 HOH HOH . 
R 10 HOH A 23 423 143 HOH HOH . 
R 10 HOH A 24 424 89 HOH HOH . 
R 10 HOH A 25 425 76 HOH HOH . 
R 10 HOH A 26 426 29 HOH HOH . 
R 10 HOH A 27 427 120 HOH HOH . 
R 10 HOH A 28 428 79 HOH HOH . 
R 10 HOH A 29 429 11 HOH HOH . 
R 10 HOH A 30 430 17 HOH HOH . 
R 10 HOH A 31 431 106 HOH HOH . 
R 10 HOH A 32 432 4 HOH HOH . 
R 10 HOH A 33 433 85 HOH HOH . 
R 10 HOH A 34 434 18 HOH HOH . 
R 10 HOH A 35 435 87 HOH HOH . 
R 10 HOH A 36 436 151 HOH HOH . 
R 10 HOH A 37 437 78 HOH HOH . 
R 10 HOH A 38 438 138 HOH HOH . 
R 10 HOH A 39 439 30 HOH HOH . 
R 10 HOH A 40 440 107 HOH HOH . 
R 10 HOH A 41 441 93 HOH HOH . 
R 10 HOH A 42 442 49 HOH HOH . 
R 10 HOH A 43 443 145 HOH HOH . 
R 10 HOH A 44 444 50 HOH HOH . 
R 10 HOH A 45 445 72 HOH HOH . 
R 10 HOH A 46 446 33 HOH HOH . 
R 10 HOH A 47 447 38 HOH HOH . 
R 10 HOH A 48 448 90 HOH HOH . 
R 10 HOH A 49 449 116 HOH HOH . 
R 10 HOH A 50 450 100 HOH HOH . 
R 10 HOH A 51 451 112 HOH HOH . 
R 10 HOH A 52 452 153 HOH HOH . 
R 10 HOH A 53 453 53 HOH HOH . 
R 10 HOH A 54 454 154 HOH HOH . 
R 10 HOH A 55 455 52 HOH HOH . 
R 10 HOH A 56 456 81 HOH HOH . 
R 10 HOH A 57 457 134 HOH HOH . 
R 10 HOH A 58 458 12 HOH HOH . 
R 10 HOH A 59 459 68 HOH HOH . 
R 10 HOH A 60 460 105 HOH HOH . 
R 10 HOH A 61 461 92 HOH HOH . 
R 10 HOH A 62 462 152 HOH HOH . 
R 10 HOH A 63 463 26 HOH HOH . 
R 10 HOH A 64 464 25 HOH HOH . 
R 10 HOH A 65 465 35 HOH HOH . 
R 10 HOH A 66 466 127 HOH HOH . 
R 10 HOH A 67 467 118 HOH HOH . 
R 10 HOH A 68 468 155 HOH HOH . 
R 10 HOH A 69 469 69 HOH HOH . 
R 10 HOH A 70 470 36 HOH HOH . 
R 10 HOH A 71 471 111 HOH HOH . 
R 10 HOH A 72 472 65 HOH HOH . 
R 10 HOH A 73 473 135 HOH HOH . 
R 10 HOH A 74 474 94 HOH HOH . 
R 10 HOH A 75 475 77 HOH HOH . 
R 10 HOH A 76 476 101 HOH HOH . 
R 10 HOH A 77 477 115 HOH HOH . 
R 10 HOH A 78 478 57 HOH HOH . 
R 10 HOH A 79 479 47 HOH HOH . 
R 10 HOH A 80 480 129 HOH HOH . 
R 10 HOH A 81 481 130 HOH HOH . 
R 10 HOH A 82 482 109 HOH HOH . 
R 10 HOH A 83 483 104 HOH HOH . 
R 10 HOH A 84 484 124 HOH HOH . 
R 10 HOH A 85 485 123 HOH HOH . 
R 10 HOH A 86 486 71 HOH HOH . 
S 10 HOH B 1 401 14 HOH HOH . 
S 10 HOH B 2 402 10 HOH HOH . 
S 10 HOH B 3 403 80 HOH HOH . 
S 10 HOH B 4 404 126 HOH HOH . 
S 10 HOH B 5 405 43 HOH HOH . 
S 10 HOH B 6 406 117 HOH HOH . 
S 10 HOH B 7 407 3 HOH HOH . 
S 10 HOH B 8 408 22 HOH HOH . 
S 10 HOH B 9 409 5 HOH HOH . 
S 10 HOH B 10 410 6 HOH HOH . 
S 10 HOH B 11 411 20 HOH HOH . 
S 10 HOH B 12 412 82 HOH HOH . 
S 10 HOH B 13 413 45 HOH HOH . 
S 10 HOH B 14 414 99 HOH HOH . 
S 10 HOH B 15 415 83 HOH HOH . 
S 10 HOH B 16 416 144 HOH HOH . 
S 10 HOH B 17 417 98 HOH HOH . 
S 10 HOH B 18 418 56 HOH HOH . 
S 10 HOH B 19 419 84 HOH HOH . 
S 10 HOH B 20 420 23 HOH HOH . 
S 10 HOH B 21 421 15 HOH HOH . 
S 10 HOH B 22 422 51 HOH HOH . 
S 10 HOH B 23 423 113 HOH HOH . 
S 10 HOH B 24 424 58 HOH HOH . 
S 10 HOH B 25 425 75 HOH HOH . 
S 10 HOH B 26 426 2 HOH HOH . 
S 10 HOH B 27 427 62 HOH HOH . 
S 10 HOH B 28 428 21 HOH HOH . 
S 10 HOH B 29 429 28 HOH HOH . 
S 10 HOH B 30 430 60 HOH HOH . 
S 10 HOH B 31 431 66 HOH HOH . 
S 10 HOH B 32 432 91 HOH HOH . 
S 10 HOH B 33 433 34 HOH HOH . 
S 10 HOH B 34 434 150 HOH HOH . 
S 10 HOH B 35 435 114 HOH HOH . 
S 10 HOH B 36 436 39 HOH HOH . 
S 10 HOH B 37 437 73 HOH HOH . 
S 10 HOH B 38 438 157 HOH HOH . 
S 10 HOH B 39 439 136 HOH HOH . 
S 10 HOH B 40 440 1 HOH HOH . 
S 10 HOH B 41 441 140 HOH HOH . 
S 10 HOH B 42 442 37 HOH HOH . 
S 10 HOH B 43 443 24 HOH HOH . 
S 10 HOH B 44 444 121 HOH HOH . 
S 10 HOH B 45 445 86 HOH HOH . 
S 10 HOH B 46 446 110 HOH HOH . 
S 10 HOH B 47 447 108 HOH HOH . 
S 10 HOH B 48 448 70 HOH HOH . 
S 10 HOH B 49 449 63 HOH HOH . 
S 10 HOH B 50 450 128 HOH HOH . 
S 10 HOH B 51 451 41 HOH HOH . 
S 10 HOH B 52 452 158 HOH HOH . 
S 10 HOH B 53 453 103 HOH HOH . 
S 10 HOH B 54 454 97 HOH HOH . 
S 10 HOH B 55 455 119 HOH HOH . 
S 10 HOH B 56 456 95 HOH HOH . 
S 10 HOH B 57 457 61 HOH HOH . 
S 10 HOH B 58 458 44 HOH HOH . 
S 10 HOH B 59 459 156 HOH HOH . 
T 10 HOH C 1 201 141 HOH HOH . 
T 10 HOH C 2 202 16 HOH HOH . 
T 10 HOH C 3 203 148 HOH HOH . 
T 10 HOH C 4 204 64 HOH HOH . 
T 10 HOH C 5 205 137 HOH HOH . 
T 10 HOH C 6 206 122 HOH HOH . 
T 10 HOH C 7 207 9 HOH HOH . 
T 10 HOH C 8 208 46 HOH HOH . 
T 10 HOH C 9 209 133 HOH HOH . 
T 10 HOH C 10 210 147 HOH HOH . 
T 10 HOH C 11 211 132 HOH HOH . 
T 10 HOH C 12 212 125 HOH HOH . 
T 10 HOH C 13 213 139 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 . . . H 7 17.301 126.27 76.057 1 45.34 ? C1 EDO 302 A 1 
HETATM 2 O O1 EDO . . . H 7 17.494 127.294 75.071 1 44.17 ? O1 EDO 302 A 1 
HETATM 3 C C2 EDO . . . H 7 16.002 126.517 76.816 1 47.22 ? C2 EDO 302 A 1 
HETATM 4 O O2 EDO . . . H 7 15.945 125.673 77.972 1 46.45 ? O2 EDO 302 A 1 
#
_model_server_stats.io_time_ms              19 
_model_server_stats.parse_time_ms           19 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           402 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           4 
#