data_3VB4
#
_model_server_result.job_id            yYnTQiKOUNxGU-8t5mZvgw 
_model_server_result.datetime_utc      '2024-12-18 04:28:13' 
_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          3vb4 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"K","auth_seq_id":404}' 
#
_entry.id    3VB4 
#
_exptl.entry_id    3VB4 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              92.094 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            GLYCEROL 
_entity.pdbx_number_of_molecules    1 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          103.17 
_cell.angle_gamma         90 
_cell.entry_id            3VB4 
_cell.length_a            52.322 
_cell.length_b            97.103 
_cell.length_c            67.405 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3VB4 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
_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,F,G,H,I,J,K,L,M,N,O 
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      4 
_struct_asym.id                             K 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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 SG CYS 145 A CYS 145 1_555 C C 0JU 5 E 0JU 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.667 ? 
covale ? covale2 B SG CYS 145 B CYS 145 1_555 D C 0JU 5 F 0JU 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.649 ? 
covale ? covale3 C C BOC 1 E BOC 1 1_555 C N ALA 2 E ALA 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 sing 
covale ? covale4 C C LEU 4 E LEU 4 1_555 C N 0JU 5 E 0JU 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 sing 
covale ? covale5 D C BOC 1 F BOC 1 1_555 D N ALA 2 F ALA 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 sing 
covale ? covale6 D C LEU 4 F LEU 4 1_555 D N 0JU 5 F 0JU 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 sing 
#
_chem_comp.formula           'C3 H8 O3' 
_chem_comp.formula_weight    92.094 
_chem_comp.id                GOL 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              GLYCEROL 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     GLYCERIN;PROPANE-1,2,3-TRIOL 
#
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 GOL sing 174 n n 
C1 C2 GOL sing 175 n n 
C1 H11 GOL sing 176 n n 
C1 H12 GOL sing 177 n n 
O1 HO1 GOL sing 178 n n 
C2 O2 GOL sing 179 n n 
C2 C3 GOL sing 180 n n 
C2 H2 GOL sing 181 n n 
O2 HO2 GOL sing 182 n n 
C3 O3 GOL sing 183 n n 
C3 H31 GOL sing 184 n n 
C3 H32 GOL sing 185 n n 
O3 HO3 GOL sing 186 n n 
#
_atom_sites.entry_id                     3VB4 
_atom_sites.fract_transf_matrix[1][1]    0.019112 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.004472 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.010298 
_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]    0.015236 
_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
E 3 EDO A 1 401 1 EDO EDO . 
F 3 EDO A 1 402 2 EDO EDO . 
G 3 EDO A 1 403 5 EDO EDO . 
H 3 EDO B 1 401 3 EDO EDO . 
I 3 EDO B 1 402 4 EDO EDO . 
J 3 EDO B 1 403 6 EDO EDO . 
K 4 GOL B 1 404 7 GOL GOL . 
L 3 EDO B 1 405 8 EDO EDO . 
M 3 EDO B 1 406 9 EDO EDO . 
N 5 HOH A 1 501 3 HOH HOH . 
N 5 HOH A 2 502 4 HOH HOH . 
N 5 HOH A 3 503 5 HOH HOH . 
N 5 HOH A 4 504 7 HOH HOH . 
N 5 HOH A 5 505 9 HOH HOH . 
N 5 HOH A 6 506 10 HOH HOH . 
N 5 HOH A 7 507 16 HOH HOH . 
N 5 HOH A 8 508 20 HOH HOH . 
N 5 HOH A 9 509 22 HOH HOH . 
N 5 HOH A 10 510 31 HOH HOH . 
N 5 HOH A 11 511 32 HOH HOH . 
N 5 HOH A 12 512 37 HOH HOH . 
N 5 HOH A 13 513 45 HOH HOH . 
N 5 HOH A 14 514 51 HOH HOH . 
N 5 HOH A 15 515 52 HOH HOH . 
N 5 HOH A 16 516 53 HOH HOH . 
N 5 HOH A 17 517 61 HOH HOH . 
N 5 HOH A 18 518 64 HOH HOH . 
N 5 HOH A 19 519 65 HOH HOH . 
N 5 HOH A 20 520 68 HOH HOH . 
N 5 HOH A 21 521 69 HOH HOH . 
N 5 HOH A 22 522 73 HOH HOH . 
N 5 HOH A 23 523 74 HOH HOH . 
N 5 HOH A 24 524 76 HOH HOH . 
N 5 HOH A 25 525 82 HOH HOH . 
N 5 HOH A 26 526 91 HOH HOH . 
N 5 HOH A 27 527 94 HOH HOH . 
N 5 HOH A 28 528 98 HOH HOH . 
N 5 HOH A 29 529 101 HOH HOH . 
N 5 HOH A 30 530 103 HOH HOH . 
N 5 HOH A 31 531 107 HOH HOH . 
N 5 HOH A 32 532 109 HOH HOH . 
N 5 HOH A 33 533 110 HOH HOH . 
N 5 HOH A 34 534 111 HOH HOH . 
N 5 HOH A 35 535 115 HOH HOH . 
N 5 HOH A 36 536 120 HOH HOH . 
N 5 HOH A 37 537 124 HOH HOH . 
N 5 HOH A 38 538 128 HOH HOH . 
N 5 HOH A 39 539 129 HOH HOH . 
N 5 HOH A 40 540 133 HOH HOH . 
N 5 HOH A 41 541 138 HOH HOH . 
N 5 HOH A 42 542 140 HOH HOH . 
N 5 HOH A 43 543 144 HOH HOH . 
N 5 HOH A 44 544 147 HOH HOH . 
N 5 HOH A 45 545 153 HOH HOH . 
N 5 HOH A 46 546 155 HOH HOH . 
N 5 HOH A 47 547 156 HOH HOH . 
N 5 HOH A 48 548 157 HOH HOH . 
N 5 HOH A 49 549 163 HOH HOH . 
N 5 HOH A 50 550 164 HOH HOH . 
N 5 HOH A 51 551 165 HOH HOH . 
N 5 HOH A 52 552 168 HOH HOH . 
N 5 HOH A 53 553 170 HOH HOH . 
N 5 HOH A 54 554 172 HOH HOH . 
N 5 HOH A 55 555 178 HOH HOH . 
N 5 HOH A 56 556 179 HOH HOH . 
N 5 HOH A 57 557 183 HOH HOH . 
N 5 HOH A 58 558 184 HOH HOH . 
N 5 HOH A 59 559 189 HOH HOH . 
N 5 HOH A 60 560 207 HOH HOH . 
N 5 HOH A 61 561 209 HOH HOH . 
N 5 HOH A 62 562 217 HOH HOH . 
N 5 HOH A 63 563 227 HOH HOH . 
N 5 HOH A 64 564 228 HOH HOH . 
N 5 HOH A 65 565 233 HOH HOH . 
N 5 HOH A 66 566 235 HOH HOH . 
N 5 HOH A 67 567 239 HOH HOH . 
N 5 HOH A 68 568 246 HOH HOH . 
N 5 HOH A 69 569 247 HOH HOH . 
N 5 HOH A 70 570 253 HOH HOH . 
N 5 HOH A 71 571 254 HOH HOH . 
N 5 HOH A 72 572 257 HOH HOH . 
N 5 HOH A 73 573 258 HOH HOH . 
N 5 HOH A 74 574 259 HOH HOH . 
N 5 HOH A 75 575 264 HOH HOH . 
N 5 HOH A 76 576 266 HOH HOH . 
N 5 HOH A 77 577 267 HOH HOH . 
N 5 HOH A 78 578 268 HOH HOH . 
N 5 HOH A 79 579 269 HOH HOH . 
N 5 HOH A 80 580 274 HOH HOH . 
N 5 HOH A 81 581 289 HOH HOH . 
N 5 HOH A 82 582 295 HOH HOH . 
N 5 HOH A 83 583 297 HOH HOH . 
N 5 HOH A 84 584 298 HOH HOH . 
N 5 HOH A 85 585 299 HOH HOH . 
N 5 HOH A 86 586 300 HOH HOH . 
N 5 HOH A 87 587 301 HOH HOH . 
N 5 HOH A 88 588 302 HOH HOH . 
N 5 HOH A 89 589 314 HOH HOH . 
N 5 HOH A 90 590 315 HOH HOH . 
N 5 HOH A 91 591 316 HOH HOH . 
N 5 HOH A 92 592 321 HOH HOH . 
N 5 HOH A 93 593 322 HOH HOH . 
N 5 HOH A 94 594 331 HOH HOH . 
N 5 HOH A 95 595 333 HOH HOH . 
N 5 HOH A 96 596 337 HOH HOH . 
O 5 HOH B 1 501 231 HOH HOH . 
O 5 HOH B 2 502 1 HOH HOH . 
O 5 HOH B 3 503 2 HOH HOH . 
O 5 HOH B 4 504 8 HOH HOH . 
O 5 HOH B 5 505 13 HOH HOH . 
O 5 HOH B 6 506 18 HOH HOH . 
O 5 HOH B 7 507 21 HOH HOH . 
O 5 HOH B 8 508 23 HOH HOH . 
O 5 HOH B 9 509 24 HOH HOH . 
O 5 HOH B 10 510 26 HOH HOH . 
O 5 HOH B 11 511 30 HOH HOH . 
O 5 HOH B 12 512 35 HOH HOH . 
O 5 HOH B 13 513 39 HOH HOH . 
O 5 HOH B 14 514 40 HOH HOH . 
O 5 HOH B 15 515 41 HOH HOH . 
O 5 HOH B 16 516 42 HOH HOH . 
O 5 HOH B 17 517 43 HOH HOH . 
O 5 HOH B 18 518 44 HOH HOH . 
O 5 HOH B 19 519 47 HOH HOH . 
O 5 HOH B 20 520 50 HOH HOH . 
O 5 HOH B 21 521 54 HOH HOH . 
O 5 HOH B 22 522 56 HOH HOH . 
O 5 HOH B 23 523 57 HOH HOH . 
O 5 HOH B 24 524 58 HOH HOH . 
O 5 HOH B 25 525 60 HOH HOH . 
O 5 HOH B 26 526 62 HOH HOH . 
O 5 HOH B 27 527 66 HOH HOH . 
O 5 HOH B 28 528 70 HOH HOH . 
O 5 HOH B 29 529 71 HOH HOH . 
O 5 HOH B 30 530 75 HOH HOH . 
O 5 HOH B 31 531 77 HOH HOH . 
O 5 HOH B 32 532 78 HOH HOH . 
O 5 HOH B 33 533 80 HOH HOH . 
O 5 HOH B 34 534 81 HOH HOH . 
O 5 HOH B 35 535 83 HOH HOH . 
O 5 HOH B 36 536 87 HOH HOH . 
O 5 HOH B 37 537 88 HOH HOH . 
O 5 HOH B 38 538 89 HOH HOH . 
O 5 HOH B 39 539 90 HOH HOH . 
O 5 HOH B 40 540 92 HOH HOH . 
O 5 HOH B 41 541 102 HOH HOH . 
O 5 HOH B 42 542 104 HOH HOH . 
O 5 HOH B 43 543 106 HOH HOH . 
O 5 HOH B 44 544 112 HOH HOH . 
O 5 HOH B 45 545 117 HOH HOH . 
O 5 HOH B 46 546 118 HOH HOH . 
O 5 HOH B 47 547 119 HOH HOH . 
O 5 HOH B 48 548 123 HOH HOH . 
O 5 HOH B 49 549 126 HOH HOH . 
O 5 HOH B 50 550 127 HOH HOH . 
O 5 HOH B 51 551 130 HOH HOH . 
O 5 HOH B 52 552 132 HOH HOH . 
O 5 HOH B 53 553 137 HOH HOH . 
O 5 HOH B 54 554 141 HOH HOH . 
O 5 HOH B 55 555 145 HOH HOH . 
O 5 HOH B 56 556 148 HOH HOH . 
O 5 HOH B 57 557 149 HOH HOH . 
O 5 HOH B 58 558 158 HOH HOH . 
O 5 HOH B 59 559 159 HOH HOH . 
O 5 HOH B 60 560 162 HOH HOH . 
O 5 HOH B 61 561 173 HOH HOH . 
O 5 HOH B 62 562 174 HOH HOH . 
O 5 HOH B 63 563 176 HOH HOH . 
O 5 HOH B 64 564 182 HOH HOH . 
O 5 HOH B 65 565 187 HOH HOH . 
O 5 HOH B 66 566 190 HOH HOH . 
O 5 HOH B 67 567 192 HOH HOH . 
O 5 HOH B 68 568 197 HOH HOH . 
O 5 HOH B 69 569 208 HOH HOH . 
O 5 HOH B 70 570 210 HOH HOH . 
O 5 HOH B 71 571 211 HOH HOH . 
O 5 HOH B 72 572 213 HOH HOH . 
O 5 HOH B 73 573 216 HOH HOH . 
O 5 HOH B 74 574 220 HOH HOH . 
O 5 HOH B 75 575 226 HOH HOH . 
O 5 HOH B 76 576 229 HOH HOH . 
O 5 HOH B 77 577 232 HOH HOH . 
O 5 HOH B 78 578 237 HOH HOH . 
O 5 HOH B 79 579 242 HOH HOH . 
O 5 HOH B 80 580 250 HOH HOH . 
O 5 HOH B 81 581 251 HOH HOH . 
O 5 HOH B 82 582 260 HOH HOH . 
O 5 HOH B 83 583 261 HOH HOH . 
O 5 HOH B 84 584 262 HOH HOH . 
O 5 HOH B 85 585 263 HOH HOH . 
O 5 HOH B 86 586 270 HOH HOH . 
O 5 HOH B 87 587 271 HOH HOH . 
O 5 HOH B 88 588 273 HOH HOH . 
O 5 HOH B 89 589 279 HOH HOH . 
O 5 HOH B 90 590 286 HOH HOH . 
O 5 HOH B 91 591 287 HOH HOH . 
O 5 HOH B 92 592 294 HOH HOH . 
O 5 HOH B 93 593 304 HOH HOH . 
O 5 HOH B 94 594 305 HOH HOH . 
O 5 HOH B 95 595 306 HOH HOH . 
O 5 HOH B 96 596 307 HOH HOH . 
O 5 HOH B 97 597 312 HOH HOH . 
O 5 HOH B 98 598 318 HOH HOH . 
O 5 HOH B 99 599 319 HOH HOH . 
O 5 HOH B 100 600 320 HOH HOH . 
O 5 HOH B 101 601 323 HOH HOH . 
O 5 HOH B 102 602 324 HOH HOH . 
O 5 HOH B 103 603 326 HOH HOH . 
O 5 HOH B 104 604 335 HOH HOH . 
O 5 HOH B 105 605 338 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 GOL . . . K 4 32.679 -5.771 14.389 1 37.79 ? C1 GOL 404 B 1 
HETATM 2 O O1 GOL . . . K 4 32.878 -4.374 14.327 1 43.34 ? O1 GOL 404 B 1 
HETATM 3 C C2 GOL . . . K 4 32.436 -6.134 15.847 1 39.84 ? C2 GOL 404 B 1 
HETATM 4 O O2 GOL . . . K 4 33.629 -6.674 16.373 1 44.39 ? O2 GOL 404 B 1 
HETATM 5 C C3 GOL . . . K 4 31.267 -7.115 15.947 1 37.79 ? C3 GOL 404 B 1 
HETATM 6 O O3 GOL . . . K 4 30.905 -7.338 17.296 1 37.01 ? O3 GOL 404 B 1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    28 
_model_server_stats.query_time_ms           228 
_model_server_stats.encode_time_ms          9 
_model_server_stats.element_count           6 
#