data_7YVR
#
_model_server_result.job_id            U5ekjAmwFEfv9mlXylvUQQ 
_model_server_result.datetime_utc      '2025-08-31 22:39:08' 
_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          7yvr 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":401}' 
#
_entry.id    7YVR 
#
_exptl.entry_id    7YVR 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              92.094 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            GLYCEROL 
_entity.pdbx_number_of_molecules    3 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          106.087 
_cell.angle_gamma         90 
_cell.entry_id            7YVR 
_cell.length_a            264.43 
_cell.length_b            59.859 
_cell.length_c            95.112 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7YVR 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    'C 2y' 
_symmetry.space_group_name_H-M     'C 1 2 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 
_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
? 2 E N N 
? 2 F N N 
? 2 G 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
covale ? covale1 A C THR 213 A THR 213 1_555 A N LLP 214 A LLP 214 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? 
covale ? covale2 A C LLP 214 A LLP 214 1_555 A N ASN 215 A ASN 215 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? 
covale ? covale3 B C THR 213 B THR 213 1_555 B N LLP 214 B LLP 214 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? 
covale ? covale4 B C LLP 214 B LLP 214 1_555 B N ASN 215 B ASN 215 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? 
covale ? covale5 C C THR 213 C THR 213 1_555 C N LLP 214 C LLP 214 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? 
covale ? covale6 C C LLP 214 C LLP 214 1_555 C N ASN 215 C ASN 215 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? 
covale ? covale7 D C THR 213 D THR 213 1_555 D N LLP 214 D LLP 214 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? 
covale ? covale8 D C LLP 214 D LLP 214 1_555 D N ASN 215 D ASN 215 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? 
#
_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 129 n n 
C1 C2 GOL sing 130 n n 
C1 H11 GOL sing 131 n n 
C1 H12 GOL sing 132 n n 
O1 HO1 GOL sing 133 n n 
C2 O2 GOL sing 134 n n 
C2 C3 GOL sing 135 n n 
C2 H2 GOL sing 136 n n 
O2 HO2 GOL sing 137 n n 
C3 O3 GOL sing 138 n n 
C3 H31 GOL sing 139 n n 
C3 H32 GOL sing 140 n n 
O3 HO3 GOL sing 141 n n 
#
_atom_sites.entry_id                     7YVR 
_atom_sites.fract_transf_matrix[1][1]    0.003782 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.001091 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.016706 
_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]    0.010942 
_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 2 GOL A 1 401 401 GOL GOL . 
F 2 GOL C 1 401 401 GOL GOL . 
G 2 GOL D 1 401 401 GOL GOL . 
H 3 HOH A 1 501 524 HOH HOH . 
H 3 HOH A 2 502 517 HOH HOH . 
H 3 HOH A 3 503 528 HOH HOH . 
H 3 HOH A 4 504 501 HOH HOH . 
H 3 HOH A 5 505 523 HOH HOH . 
H 3 HOH A 6 506 504 HOH HOH . 
H 3 HOH A 7 507 510 HOH HOH . 
H 3 HOH A 8 508 523 HOH HOH . 
H 3 HOH A 9 509 521 HOH HOH . 
H 3 HOH A 10 510 508 HOH HOH . 
H 3 HOH A 11 511 522 HOH HOH . 
H 3 HOH A 12 512 520 HOH HOH . 
H 3 HOH A 13 513 527 HOH HOH . 
H 3 HOH A 14 514 519 HOH HOH . 
H 3 HOH A 15 515 503 HOH HOH . 
H 3 HOH A 16 516 533 HOH HOH . 
H 3 HOH A 17 517 505 HOH HOH . 
H 3 HOH A 18 518 506 HOH HOH . 
H 3 HOH A 19 519 536 HOH HOH . 
H 3 HOH A 20 520 534 HOH HOH . 
H 3 HOH A 21 521 512 HOH HOH . 
H 3 HOH A 22 522 511 HOH HOH . 
H 3 HOH A 23 523 502 HOH HOH . 
H 3 HOH A 24 524 527 HOH HOH . 
H 3 HOH A 25 525 507 HOH HOH . 
H 3 HOH A 26 526 530 HOH HOH . 
H 3 HOH A 27 527 513 HOH HOH . 
H 3 HOH A 28 528 532 HOH HOH . 
H 3 HOH A 29 529 514 HOH HOH . 
H 3 HOH A 30 530 529 HOH HOH . 
H 3 HOH A 31 531 525 HOH HOH . 
H 3 HOH A 32 532 531 HOH HOH . 
H 3 HOH A 33 533 509 HOH HOH . 
H 3 HOH A 34 534 515 HOH HOH . 
H 3 HOH A 35 535 516 HOH HOH . 
H 3 HOH A 36 536 526 HOH HOH . 
H 3 HOH A 37 537 518 HOH HOH . 
I 3 HOH B 1 401 533 HOH HOH . 
I 3 HOH B 2 402 506 HOH HOH . 
I 3 HOH B 3 403 515 HOH HOH . 
I 3 HOH B 4 404 507 HOH HOH . 
I 3 HOH B 5 405 526 HOH HOH . 
I 3 HOH B 6 406 502 HOH HOH . 
I 3 HOH B 7 407 519 HOH HOH . 
I 3 HOH B 8 408 501 HOH HOH . 
I 3 HOH B 9 409 521 HOH HOH . 
I 3 HOH B 10 410 525 HOH HOH . 
I 3 HOH B 11 411 534 HOH HOH . 
I 3 HOH B 12 412 510 HOH HOH . 
I 3 HOH B 13 413 529 HOH HOH . 
I 3 HOH B 14 414 505 HOH HOH . 
I 3 HOH B 15 415 527 HOH HOH . 
I 3 HOH B 16 416 509 HOH HOH . 
I 3 HOH B 17 417 514 HOH HOH . 
I 3 HOH B 18 418 522 HOH HOH . 
I 3 HOH B 19 419 530 HOH HOH . 
I 3 HOH B 20 420 512 HOH HOH . 
I 3 HOH B 21 421 524 HOH HOH . 
I 3 HOH B 22 422 516 HOH HOH . 
I 3 HOH B 23 423 504 HOH HOH . 
I 3 HOH B 24 424 520 HOH HOH . 
I 3 HOH B 25 425 531 HOH HOH . 
I 3 HOH B 26 426 523 HOH HOH . 
I 3 HOH B 27 427 518 HOH HOH . 
I 3 HOH B 28 428 517 HOH HOH . 
I 3 HOH B 29 429 511 HOH HOH . 
I 3 HOH B 30 430 503 HOH HOH . 
I 3 HOH B 31 431 528 HOH HOH . 
I 3 HOH B 32 432 508 HOH HOH . 
I 3 HOH B 33 433 532 HOH HOH . 
I 3 HOH B 34 434 513 HOH HOH . 
J 3 HOH C 1 501 549 HOH HOH . 
J 3 HOH C 2 502 509 HOH HOH . 
J 3 HOH C 3 503 503 HOH HOH . 
J 3 HOH C 4 504 534 HOH HOH . 
J 3 HOH C 5 505 512 HOH HOH . 
J 3 HOH C 6 506 537 HOH HOH . 
J 3 HOH C 7 507 516 HOH HOH . 
J 3 HOH C 8 508 531 HOH HOH . 
J 3 HOH C 9 509 508 HOH HOH . 
J 3 HOH C 10 510 502 HOH HOH . 
J 3 HOH C 11 511 519 HOH HOH . 
J 3 HOH C 12 512 544 HOH HOH . 
J 3 HOH C 13 513 536 HOH HOH . 
J 3 HOH C 14 514 535 HOH HOH . 
J 3 HOH C 15 515 548 HOH HOH . 
J 3 HOH C 16 516 546 HOH HOH . 
J 3 HOH C 17 517 514 HOH HOH . 
J 3 HOH C 18 518 501 HOH HOH . 
J 3 HOH C 19 519 550 HOH HOH . 
J 3 HOH C 20 520 533 HOH HOH . 
J 3 HOH C 21 521 504 HOH HOH . 
J 3 HOH C 22 522 538 HOH HOH . 
J 3 HOH C 23 523 513 HOH HOH . 
J 3 HOH C 24 524 539 HOH HOH . 
J 3 HOH C 25 525 528 HOH HOH . 
J 3 HOH C 26 526 545 HOH HOH . 
J 3 HOH C 27 527 540 HOH HOH . 
J 3 HOH C 28 528 522 HOH HOH . 
J 3 HOH C 29 529 520 HOH HOH . 
J 3 HOH C 30 530 518 HOH HOH . 
J 3 HOH C 31 531 547 HOH HOH . 
J 3 HOH C 32 532 515 HOH HOH . 
J 3 HOH C 33 533 523 HOH HOH . 
J 3 HOH C 34 534 511 HOH HOH . 
J 3 HOH C 35 535 530 HOH HOH . 
J 3 HOH C 36 536 535 HOH HOH . 
J 3 HOH C 37 537 543 HOH HOH . 
J 3 HOH C 38 538 506 HOH HOH . 
J 3 HOH C 39 539 517 HOH HOH . 
J 3 HOH C 40 540 524 HOH HOH . 
J 3 HOH C 41 541 507 HOH HOH . 
J 3 HOH C 42 542 505 HOH HOH . 
J 3 HOH C 43 543 532 HOH HOH . 
J 3 HOH C 44 544 529 HOH HOH . 
J 3 HOH C 45 545 521 HOH HOH . 
J 3 HOH C 46 546 526 HOH HOH . 
J 3 HOH C 47 547 525 HOH HOH . 
J 3 HOH C 48 548 510 HOH HOH . 
J 3 HOH C 49 549 542 HOH HOH . 
J 3 HOH C 50 550 541 HOH HOH . 
K 3 HOH D 1 501 527 HOH HOH . 
K 3 HOH D 2 502 503 HOH HOH . 
K 3 HOH D 3 503 518 HOH HOH . 
K 3 HOH D 4 504 531 HOH HOH . 
K 3 HOH D 5 505 525 HOH HOH . 
K 3 HOH D 6 506 543 HOH HOH . 
K 3 HOH D 7 507 539 HOH HOH . 
K 3 HOH D 8 508 535 HOH HOH . 
K 3 HOH D 9 509 504 HOH HOH . 
K 3 HOH D 10 510 520 HOH HOH . 
K 3 HOH D 11 511 509 HOH HOH . 
K 3 HOH D 12 512 536 HOH HOH . 
K 3 HOH D 13 513 513 HOH HOH . 
K 3 HOH D 14 514 502 HOH HOH . 
K 3 HOH D 15 515 516 HOH HOH . 
K 3 HOH D 16 516 534 HOH HOH . 
K 3 HOH D 17 517 533 HOH HOH . 
K 3 HOH D 18 518 505 HOH HOH . 
K 3 HOH D 19 519 501 HOH HOH . 
K 3 HOH D 20 520 541 HOH HOH . 
K 3 HOH D 21 521 549 HOH HOH . 
K 3 HOH D 22 522 506 HOH HOH . 
K 3 HOH D 23 523 532 HOH HOH . 
K 3 HOH D 24 524 540 HOH HOH . 
K 3 HOH D 25 525 511 HOH HOH . 
K 3 HOH D 26 526 514 HOH HOH . 
K 3 HOH D 27 527 521 HOH HOH . 
K 3 HOH D 28 528 530 HOH HOH . 
K 3 HOH D 29 529 544 HOH HOH . 
K 3 HOH D 30 530 515 HOH HOH . 
K 3 HOH D 31 531 529 HOH HOH . 
K 3 HOH D 32 532 519 HOH HOH . 
K 3 HOH D 33 533 510 HOH HOH . 
K 3 HOH D 34 534 548 HOH HOH . 
K 3 HOH D 35 535 528 HOH HOH . 
K 3 HOH D 36 536 522 HOH HOH . 
K 3 HOH D 37 537 526 HOH HOH . 
K 3 HOH D 38 538 538 HOH HOH . 
K 3 HOH D 39 539 542 HOH HOH . 
K 3 HOH D 40 540 507 HOH HOH . 
K 3 HOH D 41 541 546 HOH HOH . 
K 3 HOH D 42 542 512 HOH HOH . 
K 3 HOH D 43 543 547 HOH HOH . 
K 3 HOH D 44 544 537 HOH HOH . 
K 3 HOH D 45 545 508 HOH HOH . 
K 3 HOH D 46 546 524 HOH HOH . 
K 3 HOH D 47 547 545 HOH HOH . 
K 3 HOH D 48 548 517 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 . . . F 2 -41.059 -17.574 -3.442 1 47.64 ? C1 GOL 401 C 1 
HETATM 2 O O1 GOL . . . F 2 -41.847 -17.75 -4.58 1 54.62 ? O1 GOL 401 C 1 
HETATM 3 C C2 GOL . . . F 2 -41.234 -16.104 -3.001 1 46.7 ? C2 GOL 401 C 1 
HETATM 4 O O2 GOL . . . F 2 -42.574 -15.755 -2.892 1 49.61 ? O2 GOL 401 C 1 
HETATM 5 C C3 GOL . . . F 2 -40.491 -16.006 -1.649 1 44.94 ? C3 GOL 401 C 1 
HETATM 6 O O3 GOL . . . F 2 -40.086 -14.679 -1.503 1 40.08 ? O3 GOL 401 C 1 
#
_model_server_stats.io_time_ms              38 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    60 
_model_server_stats.query_time_ms           411 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           6 
#