URL: https://models.rcsb.org/v1/4ia3/ligand
data_4IA3
#
_model_server_result.job_id 7hCVtzJIeFVRZvxl0Kulbg
_model_server_result.datetime_utc '2026-04-04 17:42:36'
_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 4ia3
#
_entry.id 4IA3
#
_exptl.entry_id 4IA3
_exptl.method 'X-RAY DIFFRACTION'
#
_entity.details ?
_entity.formula_weight 33916.543
_entity.id 1
_entity.src_method man
_entity.type polymer
_entity.pdbx_description 'Vitamin D3 receptor A'
_entity.pdbx_number_of_molecules 1
_entity.pdbx_parent_entity_id .
_entity.pdbx_mutation ?
_entity.pdbx_fragment 'Ligand binding domain (unp residues 156-453)'
_entity.pdbx_ec ?
#
_cell.angle_alpha 90
_cell.angle_beta 90
_cell.angle_gamma 120
_cell.entry_id 4IA3
_cell.length_a 66.044
_cell.length_b 66.044
_cell.length_c 266.634
_cell.Z_PDB 12
_cell.pdbx_unique_axis ?
#
_symmetry.entry_id 4IA3
_symmetry.cell_setting ?
_symmetry.Int_Tables_number 179
_symmetry.space_group_name_Hall ?
_symmetry.space_group_name_H-M 'P 65 2 2'
#
_pdbx_struct_assembly.method_details PISA
_pdbx_struct_assembly.oligomeric_details tetrameric
_pdbx_struct_assembly.oligomeric_count 4
_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
_pdbx_struct_assembly_gen.assembly_id 1
_pdbx_struct_assembly_gen.oper_expression 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' 10_665 -y+1,-x+1,-z+1/6 0.5 -0.866025 0 -0.866025 -0.5 0 0 0 -1 33.022 57.195782 44.439
#
_struct_asym.details ?
_struct_asym.entity_id 1
_struct_asym.id A
_struct_asym.pdbx_modified N
_struct_asym.pdbx_blank_PDB_chainid_flag N
#
_entity_poly.entity_id 1
_entity_poly.nstd_linkage no
_entity_poly.nstd_monomer no
_entity_poly.type polypeptide(L)
_entity_poly.pdbx_strand_id A
_entity_poly.pdbx_seq_one_letter_code
;HMLSDEQMQIINSLVEAHHKTYDDSYSDFVRFRPPVREGPVTRSASRAASLHSLSDASSDSFNHSPESVDTKLNFSNLLM
MYQDSGSPDSSEEDQQSRLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTAEDQIALLKSSAIEIIMLRSNQSFSLEDMS
WSCGGPDFKYCINDVTKAGHTLELLEPLVKFQVGLKKLKLHEEEHVLLMAICLLSPDRPGVQDHVRIEALQDRLCDVLQA
YIRIQHPGGRLLYAKMIQKLADLRSLNEEHSKQYRSLSFQPEHSMQLTPLVLEVFGSEVS
;
_entity_poly.pdbx_seq_one_letter_code_can
;HMLSDEQMQIINSLVEAHHKTYDDSYSDFVRFRPPVREGPVTRSASRAASLHSLSDASSDSFNHSPESVDTKLNFSNLLM
MYQDSGSPDSSEEDQQSRLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTAEDQIALLKSSAIEIIMLRSNQSFSLEDMS
WSCGGPDFKYCINDVTKAGHTLELLEPLVKFQVGLKKLKLHEEEHVLLMAICLLSPDRPGVQDHVRIEALQDRLCDVLQA
YIRIQHPGGRLLYAKMIQKLADLRSLNEEHSKQYRSLSFQPEHSMQLTPLVLEVFGSEVS
;
_entity_poly.pdbx_target_identifier ?
#
loop_
_entity_poly_seq.entity_id
_entity_poly_seq.hetero
_entity_poly_seq.mon_id
_entity_poly_seq.num
1 n HIS 1
1 n MET 2
1 n LEU 3
1 n SER 4
1 n ASP 5
1 n GLU 6
1 n GLN 7
1 n MET 8
1 n GLN 9
1 n ILE 10
1 n ILE 11
1 n ASN 12
1 n SER 13
1 n LEU 14
1 n VAL 15
1 n GLU 16
1 n ALA 17
1 n HIS 18
1 n HIS 19
1 n LYS 20
1 n THR 21
1 n TYR 22
1 n ASP 23
1 n ASP 24
1 n SER 25
1 n TYR 26
1 n SER 27
1 n ASP 28
1 n PHE 29
1 n VAL 30
1 n ARG 31
1 n PHE 32
1 n ARG 33
1 n PRO 34
1 n PRO 35
1 n VAL 36
1 n ARG 37
1 n GLU 38
1 n GLY 39
1 n PRO 40
1 n VAL 41
1 n THR 42
1 n ARG 43
1 n SER 44
1 n ALA 45
1 n SER 46
1 n ARG 47
1 n ALA 48
1 n ALA 49
1 n SER 50
1 n LEU 51
1 n HIS 52
1 n SER 53
1 n LEU 54
1 n SER 55
1 n ASP 56
1 n ALA 57
1 n SER 58
1 n SER 59
1 n ASP 60
1 n SER 61
1 n PHE 62
1 n ASN 63
1 n HIS 64
1 n SER 65
1 n PRO 66
1 n GLU 67
1 n SER 68
1 n VAL 69
1 n ASP 70
1 n THR 71
1 n LYS 72
1 n LEU 73
1 n ASN 74
1 n PHE 75
1 n SER 76
1 n ASN 77
1 n LEU 78
1 n LEU 79
1 n MET 80
1 n MET 81
1 n TYR 82
1 n GLN 83
1 n ASP 84
1 n SER 85
1 n GLY 86
1 n SER 87
1 n PRO 88
1 n ASP 89
1 n SER 90
1 n SER 91
1 n GLU 92
1 n GLU 93
1 n ASP 94
1 n GLN 95
1 n GLN 96
1 n SER 97
1 n ARG 98
1 n LEU 99
1 n SER 100
1 n MET 101
1 n LEU 102
1 n PRO 103
1 n HIS 104
1 n LEU 105
1 n ALA 106
1 n ASP 107
1 n LEU 108
1 n VAL 109
1 n SER 110
1 n TYR 111
1 n SER 112
1 n ILE 113
1 n GLN 114
1 n LYS 115
1 n VAL 116
1 n ILE 117
1 n GLY 118
1 n PHE 119
1 n ALA 120
1 n LYS 121
1 n MET 122
1 n ILE 123
1 n PRO 124
1 n GLY 125
1 n PHE 126
1 n ARG 127
1 n ASP 128
1 n LEU 129
1 n THR 130
1 n ALA 131
1 n GLU 132
1 n ASP 133
1 n GLN 134
1 n ILE 135
1 n ALA 136
1 n LEU 137
1 n LEU 138
1 n LYS 139
1 n SER 140
1 n SER 141
1 n ALA 142
1 n ILE 143
1 n GLU 144
1 n ILE 145
1 n ILE 146
1 n MET 147
1 n LEU 148
1 n ARG 149
1 n SER 150
1 n ASN 151
1 n GLN 152
1 n SER 153
1 n PHE 154
1 n SER 155
1 n LEU 156
1 n GLU 157
1 n ASP 158
1 n MET 159
1 n SER 160
1 n TRP 161
1 n SER 162
1 n CYS 163
1 n GLY 164
1 n GLY 165
1 n PRO 166
1 n ASP 167
1 n PHE 168
1 n LYS 169
1 n TYR 170
1 n CYS 171
1 n ILE 172
1 n ASN 173
1 n ASP 174
1 n VAL 175
1 n THR 176
1 n LYS 177
1 n ALA 178
1 n GLY 179
1 n HIS 180
1 n THR 181
1 n LEU 182
1 n GLU 183
1 n LEU 184
1 n LEU 185
1 n GLU 186
1 n PRO 187
1 n LEU 188
1 n VAL 189
1 n LYS 190
1 n PHE 191
1 n GLN 192
1 n VAL 193
1 n GLY 194
1 n LEU 195
1 n LYS 196
1 n LYS 197
1 n LEU 198
1 n LYS 199
1 n LEU 200
1 n HIS 201
1 n GLU 202
1 n GLU 203
1 n GLU 204
1 n HIS 205
1 n VAL 206
1 n LEU 207
1 n LEU 208
1 n MET 209
1 n ALA 210
1 n ILE 211
1 n CYS 212
1 n LEU 213
1 n LEU 214
1 n SER 215
1 n PRO 216
1 n ASP 217
1 n ARG 218
1 n PRO 219
1 n GLY 220
1 n VAL 221
1 n GLN 222
1 n ASP 223
1 n HIS 224
1 n VAL 225
1 n ARG 226
1 n ILE 227
1 n GLU 228
1 n ALA 229
1 n LEU 230
1 n GLN 231
1 n ASP 232
1 n ARG 233
1 n LEU 234
1 n CYS 235
1 n ASP 236
1 n VAL 237
1 n LEU 238
1 n GLN 239
1 n ALA 240
1 n TYR 241
1 n ILE 242
1 n ARG 243
1 n ILE 244
1 n GLN 245
1 n HIS 246
1 n PRO 247
1 n GLY 248
1 n GLY 249
1 n ARG 250
1 n LEU 251
1 n LEU 252
1 n TYR 253
1 n ALA 254
1 n LYS 255
1 n MET 256
1 n ILE 257
1 n GLN 258
1 n LYS 259
1 n LEU 260
1 n ALA 261
1 n ASP 262
1 n LEU 263
1 n ARG 264
1 n SER 265
1 n LEU 266
1 n ASN 267
1 n GLU 268
1 n GLU 269
1 n HIS 270
1 n SER 271
1 n LYS 272
1 n GLN 273
1 n TYR 274
1 n ARG 275
1 n SER 276
1 n LEU 277
1 n SER 278
1 n PHE 279
1 n GLN 280
1 n PRO 281
1 n GLU 282
1 n HIS 283
1 n SER 284
1 n MET 285
1 n GLN 286
1 n LEU 287
1 n THR 288
1 n PRO 289
1 n LEU 290
1 n VAL 291
1 n LEU 292
1 n GLU 293
1 n VAL 294
1 n PHE 295
1 n GLY 296
1 n SER 297
1 n GLU 298
1 n VAL 299
1 n SER 300
#
_chem_comp.formula 'C6 H10 N3 O2 1'
_chem_comp.formula_weight 156.162
_chem_comp.id HIS
_chem_comp.mon_nstd_flag y
_chem_comp.name HISTIDINE
_chem_comp.type 'l-peptide linking'
_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
N CA HIS sing 221 n n
N H HIS sing 222 n n
N H2 HIS sing 223 n n
CA C HIS sing 224 n n
CA CB HIS sing 225 n n
CA HA HIS sing 226 n n
C O HIS doub 227 n n
C OXT HIS sing 228 n n
CB CG HIS sing 229 n n
CB HB2 HIS sing 230 n n
CB HB3 HIS sing 231 n n
CG ND1 HIS sing 232 n y
CG CD2 HIS doub 233 n y
ND1 CE1 HIS doub 234 n y
ND1 HD1 HIS sing 235 n n
CD2 NE2 HIS sing 236 n y
CD2 HD2 HIS sing 237 n n
CE1 NE2 HIS sing 238 n y
CE1 HE1 HIS sing 239 n n
NE2 HE2 HIS sing 240 n n
OXT HXT HIS sing 241 n n
#
_atom_sites.entry_id 4IA3
_atom_sites.fract_transf_matrix[1][1] 0.015141
_atom_sites.fract_transf_matrix[1][2] 0.008742
_atom_sites.fract_transf_matrix[1][3] 0
_atom_sites.fract_transf_matrix[2][1] 0
_atom_sites.fract_transf_matrix[2][2] 0.017484
_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] 0.00375
_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 3 BIV A 1 501 1 BIV LI7 ?
D 4 HOH A 1 601 1 HOH TIP ?
D 4 HOH A 2 602 2 HOH TIP ?
D 4 HOH A 3 603 3 HOH TIP ?
D 4 HOH A 4 604 4 HOH TIP ?
D 4 HOH A 5 605 5 HOH TIP ?
D 4 HOH A 6 606 6 HOH TIP ?
D 4 HOH A 7 607 7 HOH TIP ?
D 4 HOH A 8 608 8 HOH TIP ?
D 4 HOH A 9 609 9 HOH TIP ?
D 4 HOH A 10 610 10 HOH TIP ?
D 4 HOH A 11 611 11 HOH TIP ?
D 4 HOH A 12 612 12 HOH TIP ?
D 4 HOH A 13 613 13 HOH TIP ?
D 4 HOH A 14 614 14 HOH TIP ?
D 4 HOH A 15 615 15 HOH TIP ?
D 4 HOH A 16 616 16 HOH TIP ?
D 4 HOH A 17 617 17 HOH TIP ?
D 4 HOH A 18 618 18 HOH TIP ?
D 4 HOH A 19 619 19 HOH TIP ?
D 4 HOH A 20 620 20 HOH TIP ?
D 4 HOH A 21 621 21 HOH TIP ?
D 4 HOH A 22 622 22 HOH TIP ?
D 4 HOH A 23 623 23 HOH TIP ?
D 4 HOH A 24 624 24 HOH TIP ?
D 4 HOH A 25 625 25 HOH TIP ?
D 4 HOH A 26 626 26 HOH TIP ?
D 4 HOH A 27 627 27 HOH TIP ?
D 4 HOH A 28 628 28 HOH TIP ?
D 4 HOH A 29 629 29 HOH TIP ?
D 4 HOH A 30 630 30 HOH TIP ?
D 4 HOH A 31 631 32 HOH TIP ?
D 4 HOH A 32 632 33 HOH TIP ?
D 4 HOH A 33 633 34 HOH TIP ?
D 4 HOH A 34 634 35 HOH TIP ?
D 4 HOH A 35 635 36 HOH TIP ?
D 4 HOH A 36 636 37 HOH TIP ?
D 4 HOH A 37 637 38 HOH TIP ?
D 4 HOH A 38 638 39 HOH TIP ?
D 4 HOH A 39 639 40 HOH TIP ?
D 4 HOH A 40 640 41 HOH TIP ?
D 4 HOH A 41 641 43 HOH TIP ?
D 4 HOH A 42 642 44 HOH TIP ?
D 4 HOH A 43 643 45 HOH TIP ?
D 4 HOH A 44 644 46 HOH TIP ?
D 4 HOH A 45 645 47 HOH TIP ?
D 4 HOH A 46 646 48 HOH TIP ?
D 4 HOH A 47 647 49 HOH TIP ?
D 4 HOH A 48 648 50 HOH TIP ?
D 4 HOH A 49 649 52 HOH TIP ?
D 4 HOH A 50 650 53 HOH TIP ?
D 4 HOH A 51 651 54 HOH TIP ?
D 4 HOH A 52 652 55 HOH TIP ?
D 4 HOH A 53 653 56 HOH TIP ?
D 4 HOH A 54 654 57 HOH TIP ?
D 4 HOH A 55 655 58 HOH TIP ?
D 4 HOH A 56 656 59 HOH TIP ?
D 4 HOH A 57 657 60 HOH TIP ?
D 4 HOH A 58 658 61 HOH TIP ?
D 4 HOH A 59 659 62 HOH TIP ?
D 4 HOH A 60 660 63 HOH TIP ?
D 4 HOH A 61 661 64 HOH TIP ?
D 4 HOH A 62 662 65 HOH TIP ?
D 4 HOH A 63 663 66 HOH TIP ?
D 4 HOH A 64 664 68 HOH TIP ?
D 4 HOH A 65 665 69 HOH TIP ?
D 4 HOH A 66 666 71 HOH TIP ?
D 4 HOH A 67 667 72 HOH TIP ?
D 4 HOH A 68 668 73 HOH TIP ?
D 4 HOH A 69 669 74 HOH TIP ?
D 4 HOH A 70 670 75 HOH TIP ?
D 4 HOH A 71 671 76 HOH TIP ?
D 4 HOH A 72 672 77 HOH TIP ?
D 4 HOH A 73 673 78 HOH TIP ?
D 4 HOH A 74 674 79 HOH TIP ?
D 4 HOH A 75 675 80 HOH TIP ?
D 4 HOH A 76 676 81 HOH TIP ?
E 4 HOH B 1 701 31 HOH TIP ?
E 4 HOH B 2 702 42 HOH TIP ?
E 4 HOH B 3 703 51 HOH TIP ?
E 4 HOH B 4 704 67 HOH TIP ?
E 4 HOH B 5 705 70 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
ATOM 1 N N HIS 1 . . A 1 14.815 50.365 70.569 1 89.29 ? N HIS 154 A 1
ATOM 2 C CA HIS 1 . . A 1 15.838 51.226 69.917 1 90.09 ? CA HIS 154 A 1
ATOM 3 C C HIS 1 . . A 1 15.226 51.891 68.673 1 88.73 ? C HIS 154 A 1
ATOM 4 O O HIS 1 . . A 1 14.042 52.221 68.673 1 88.59 ? O HIS 154 A 1
ATOM 5 C CB HIS 1 . . A 1 17.049 50.37 69.537 1 93.08 ? CB HIS 154 A 1
ATOM 6 C CG HIS 1 . . A 1 18.275 51.165 69.211 1 96.68 ? CG HIS 154 A 1
ATOM 7 N ND1 HIS 1 . . A 1 18.866 52.022 70.115 1 97.94 ? ND1 HIS 154 A 1
ATOM 8 C CD2 HIS 1 . . A 1 19.012 51.244 68.078 1 97.33 ? CD2 HIS 154 A 1
ATOM 9 C CE1 HIS 1 . . A 1 19.913 52.598 69.551 1 98.77 ? CE1 HIS 154 A 1
ATOM 10 N NE2 HIS 1 . . A 1 20.024 52.143 68.315 1 99 ? NE2 HIS 154 A 1
#
_model_server_stats.io_time_ms 18
_model_server_stats.parse_time_ms 7
_model_server_stats.create_model_time_ms 3
_model_server_stats.query_time_ms 208
_model_server_stats.encode_time_ms 3
_model_server_stats.element_count 10
#
