data_6YEH
#
_model_server_result.job_id            GKMHTX22UAtRKjiHtRXF1A 
_model_server_result.datetime_utc      '2024-11-08 09:46:32' 
_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          6yeh 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":502}' 
#
_entry.id    6YEH 
#
_exptl.entry_id    6YEH 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              118.174 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            (4S)-2-METHYL-2,4-PENTANEDIOL 
_entity.pdbx_number_of_molecules    11 
_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            6YEH 
_cell.length_a            93.57 
_cell.length_b            99.169 
_cell.length_c            318.084 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6YEH 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    'P 2ac 2ab' 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    hexameric 
_pdbx_struct_assembly.oligomeric_count      6 
_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,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA 
_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 G N N 
? 2 H N N 
? 2 I N N 
? 2 J N N 
? 2 M N N 
? 2 O N N 
? 2 P N N 
? 2 R N N 
? 2 S N N 
? 2 U N N 
? 2 V 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
metalc ? metalc1 A O SER 30 A SER 27 1_555 K K K . A K 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.558 ? 
metalc ? metalc2 A O ILE 33 A ILE 30 1_555 K K K . A K 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.632 ? 
metalc ? metalc3 A OE2 GLU 41 A GLU 38 1_555 L K K . A K 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.563 ? 
metalc ? metalc4 K K K . A K 505 1_555 B OE2 GLU 41 B GLU 38 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.517 ? 
metalc ? metalc5 L K K . A K 506 1_555 B O SER 30 B SER 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.453 ? 
metalc ? metalc6 L K K . A K 506 1_555 B O ILE 33 B ILE 30 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.526 ? 
metalc ? metalc7 C O SER 30 C SER 27 1_555 N K K . C K 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.565 ? 
metalc ? metalc8 C O ILE 33 C ILE 30 1_555 N K K . C K 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.474 ? 
metalc ? metalc9 C OE2 GLU 41 C GLU 38 1_555 Q K K . D K 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.589 ? 
metalc ? metalc10 N K K . C K 501 1_555 Z O HOH . C HOH 610 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.358 ? 
metalc ? metalc11 N K K . C K 501 1_555 D OE2 GLU 41 D GLU 38 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.611 ? 
metalc ? metalc12 D O SER 30 D SER 27 1_555 Q K K . D K 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.551 ? 
metalc ? metalc13 D O ILE 33 D ILE 30 1_555 Q K K . D K 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.613 ? 
metalc ? metalc14 E O SER 30 E SER 27 1_555 T K K . E K 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.569 ? 
metalc ? metalc15 E O ILE 33 E ILE 30 1_555 T K K . E K 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.6 ? 
metalc ? metalc16 E OE1 GLU 41 E GLU 38 1_555 W K K . E K 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.473 ? 
metalc ? metalc17 E OE2 GLU 41 E GLU 38 1_555 W K K . E K 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.526 ? 
metalc ? metalc18 T K K . E K 502 1_555 F OE2 GLU 41 F GLU 38 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.659 ? 
metalc ? metalc19 W K K . E K 505 1_555 F O SER 30 F SER 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.622 ? 
metalc ? metalc20 W K K . E K 505 1_555 F O ILE 33 F ILE 30 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.588 ? 
#
_chem_comp.formula           'C6 H14 O2' 
_chem_comp.formula_weight    118.174 
_chem_comp.id                MPD 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              (4S)-2-METHYL-2,4-PENTANEDIOL 
_chem_comp.type              non-polymer 
_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
C1 C2 MPD sing 237 n n 
C1 H11 MPD sing 238 n n 
C1 H12 MPD sing 239 n n 
C1 H13 MPD sing 240 n n 
C2 O2 MPD sing 241 n n 
C2 CM MPD sing 242 n n 
C2 C3 MPD sing 243 n n 
O2 HO2 MPD sing 244 n n 
CM HM1 MPD sing 245 n n 
CM HM2 MPD sing 246 n n 
CM HM3 MPD sing 247 n n 
C3 C4 MPD sing 248 n n 
C3 H31 MPD sing 249 n n 
C3 H32 MPD sing 250 n n 
C4 O4 MPD sing 251 n n 
C4 C5 MPD sing 252 n n 
C4 H4 MPD sing 253 n n 
O4 HO4 MPD sing 254 n n 
C5 H51 MPD sing 255 n n 
C5 H52 MPD sing 256 n n 
C5 H53 MPD sing 257 n n 
#
_atom_sites.entry_id                     6YEH 
_atom_sites.fract_transf_matrix[1][1]    0.010687 
_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]    0.010084 
_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]    0.003144 
_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 2 MPD A 1 501 412 MPD MPD . 
H 2 MPD A 1 502 413 MPD MPD . 
I 2 MPD A 1 503 414 MPD MPD . 
J 2 MPD A 1 504 415 MPD MPD . 
K 3 K A 1 505 501 K K . 
L 3 K A 1 506 501 K K . 
M 2 MPD B 1 501 414 MPD MPD . 
N 3 K C 1 501 412 K K . 
O 2 MPD C 1 502 413 MPD MPD . 
P 2 MPD C 1 503 414 MPD MPD . 
Q 3 K D 1 501 412 K K . 
R 2 MPD D 1 502 413 MPD MPD . 
S 2 MPD E 1 501 412 MPD MPD . 
T 3 K E 1 502 413 K K . 
U 2 MPD E 1 503 414 MPD MPD . 
V 2 MPD E 1 504 415 MPD MPD . 
W 3 K E 1 505 501 K K . 
X 4 HOH A 1 601 427 HOH HOH . 
X 4 HOH A 2 602 423 HOH HOH . 
X 4 HOH A 3 603 434 HOH HOH . 
X 4 HOH A 4 604 432 HOH HOH . 
X 4 HOH A 5 605 417 HOH HOH . 
X 4 HOH A 6 606 433 HOH HOH . 
X 4 HOH A 7 607 416 HOH HOH . 
X 4 HOH A 8 608 422 HOH HOH . 
X 4 HOH A 9 609 438 HOH HOH . 
X 4 HOH A 10 610 439 HOH HOH . 
X 4 HOH A 11 611 420 HOH HOH . 
X 4 HOH A 12 612 418 HOH HOH . 
X 4 HOH A 13 613 424 HOH HOH . 
X 4 HOH A 14 614 444 HOH HOH . 
X 4 HOH A 15 615 435 HOH HOH . 
X 4 HOH A 16 616 446 HOH HOH . 
X 4 HOH A 17 617 437 HOH HOH . 
X 4 HOH A 18 618 430 HOH HOH . 
X 4 HOH A 19 619 447 HOH HOH . 
X 4 HOH A 20 620 442 HOH HOH . 
X 4 HOH A 21 621 441 HOH HOH . 
X 4 HOH A 22 622 440 HOH HOH . 
X 4 HOH A 23 623 431 HOH HOH . 
X 4 HOH A 24 624 426 HOH HOH . 
X 4 HOH A 25 625 429 HOH HOH . 
X 4 HOH A 26 626 419 HOH HOH . 
X 4 HOH A 27 627 443 HOH HOH . 
X 4 HOH A 28 628 428 HOH HOH . 
X 4 HOH A 29 629 445 HOH HOH . 
X 4 HOH A 30 630 425 HOH HOH . 
Y 4 HOH B 1 601 426 HOH HOH . 
Y 4 HOH B 2 602 437 HOH HOH . 
Y 4 HOH B 3 603 439 HOH HOH . 
Y 4 HOH B 4 604 424 HOH HOH . 
Y 4 HOH B 5 605 419 HOH HOH . 
Y 4 HOH B 6 606 418 HOH HOH . 
Y 4 HOH B 7 607 429 HOH HOH . 
Y 4 HOH B 8 608 416 HOH HOH . 
Y 4 HOH B 9 609 422 HOH HOH . 
Y 4 HOH B 10 610 428 HOH HOH . 
Y 4 HOH B 11 611 433 HOH HOH . 
Y 4 HOH B 12 612 431 HOH HOH . 
Y 4 HOH B 13 613 434 HOH HOH . 
Y 4 HOH B 14 614 415 HOH HOH . 
Y 4 HOH B 15 615 420 HOH HOH . 
Y 4 HOH B 16 616 435 HOH HOH . 
Y 4 HOH B 17 617 421 HOH HOH . 
Y 4 HOH B 18 618 425 HOH HOH . 
Y 4 HOH B 19 619 427 HOH HOH . 
Y 4 HOH B 20 620 416 HOH HOH . 
Y 4 HOH B 21 621 430 HOH HOH . 
Y 4 HOH B 22 622 438 HOH HOH . 
Y 4 HOH B 23 623 423 HOH HOH . 
Y 4 HOH B 24 624 436 HOH HOH . 
Y 4 HOH B 25 625 417 HOH HOH . 
Z 4 HOH C 1 601 434 HOH HOH . 
Z 4 HOH C 2 602 415 HOH HOH . 
Z 4 HOH C 3 603 436 HOH HOH . 
Z 4 HOH C 4 604 420 HOH HOH . 
Z 4 HOH C 5 605 422 HOH HOH . 
Z 4 HOH C 6 606 421 HOH HOH . 
Z 4 HOH C 7 607 436 HOH HOH . 
Z 4 HOH C 8 608 418 HOH HOH . 
Z 4 HOH C 9 609 431 HOH HOH . 
Z 4 HOH C 10 610 427 HOH HOH . 
Z 4 HOH C 11 611 428 HOH HOH . 
Z 4 HOH C 12 612 435 HOH HOH . 
Z 4 HOH C 13 613 419 HOH HOH . 
Z 4 HOH C 14 614 429 HOH HOH . 
Z 4 HOH C 15 615 423 HOH HOH . 
Z 4 HOH C 16 616 438 HOH HOH . 
Z 4 HOH C 17 617 417 HOH HOH . 
Z 4 HOH C 18 618 430 HOH HOH . 
Z 4 HOH C 19 619 424 HOH HOH . 
Z 4 HOH C 20 620 432 HOH HOH . 
Z 4 HOH C 21 621 433 HOH HOH . 
Z 4 HOH C 22 622 426 HOH HOH . 
Z 4 HOH C 23 623 416 HOH HOH . 
Z 4 HOH C 24 624 437 HOH HOH . 
Z 4 HOH C 25 625 428 HOH HOH . 
Z 4 HOH C 26 626 421 HOH HOH . 
Z 4 HOH C 27 627 425 HOH HOH . 
AA 4 HOH D 1 601 425 HOH HOH . 
AA 4 HOH D 2 602 422 HOH HOH . 
AA 4 HOH D 3 603 432 HOH HOH . 
AA 4 HOH D 4 604 430 HOH HOH . 
AA 4 HOH D 5 605 417 HOH HOH . 
AA 4 HOH D 6 606 415 HOH HOH . 
AA 4 HOH D 7 607 431 HOH HOH . 
AA 4 HOH D 8 608 426 HOH HOH . 
AA 4 HOH D 9 609 414 HOH HOH . 
AA 4 HOH D 10 610 423 HOH HOH . 
AA 4 HOH D 11 611 424 HOH HOH . 
AA 4 HOH D 12 612 433 HOH HOH . 
AA 4 HOH D 13 613 419 HOH HOH . 
AA 4 HOH D 14 614 429 HOH HOH . 
AA 4 HOH D 15 615 420 HOH HOH . 
AA 4 HOH D 16 616 421 HOH HOH . 
AA 4 HOH D 17 617 427 HOH HOH . 
AA 4 HOH D 18 618 432 HOH HOH . 
AA 4 HOH D 19 619 434 HOH HOH . 
AA 4 HOH D 20 620 418 HOH HOH . 
BA 4 HOH E 1 601 420 HOH HOH . 
BA 4 HOH E 2 602 426 HOH HOH . 
BA 4 HOH E 3 603 427 HOH HOH . 
BA 4 HOH E 4 604 417 HOH HOH . 
BA 4 HOH E 5 605 429 HOH HOH . 
BA 4 HOH E 6 606 424 HOH HOH . 
BA 4 HOH E 7 607 419 HOH HOH . 
BA 4 HOH E 8 608 421 HOH HOH . 
BA 4 HOH E 9 609 418 HOH HOH . 
BA 4 HOH E 10 610 432 HOH HOH . 
BA 4 HOH E 11 611 422 HOH HOH . 
BA 4 HOH E 12 612 425 HOH HOH . 
BA 4 HOH E 13 613 431 HOH HOH . 
BA 4 HOH E 14 614 430 HOH HOH . 
BA 4 HOH E 15 615 428 HOH HOH . 
BA 4 HOH E 16 616 423 HOH HOH . 
BA 4 HOH E 17 617 433 HOH HOH . 
BA 4 HOH E 18 618 434 HOH HOH . 
CA 4 HOH F 1 501 426 HOH HOH . 
CA 4 HOH F 2 502 429 HOH HOH . 
CA 4 HOH F 3 503 412 HOH HOH . 
CA 4 HOH F 4 504 427 HOH HOH . 
CA 4 HOH F 5 505 414 HOH HOH . 
CA 4 HOH F 6 506 424 HOH HOH . 
CA 4 HOH F 7 507 413 HOH HOH . 
CA 4 HOH F 8 508 417 HOH HOH . 
CA 4 HOH F 9 509 422 HOH HOH . 
CA 4 HOH F 10 510 420 HOH HOH . 
CA 4 HOH F 11 511 418 HOH HOH . 
CA 4 HOH F 12 512 421 HOH HOH . 
CA 4 HOH F 13 513 415 HOH HOH . 
CA 4 HOH F 14 514 430 HOH HOH . 
CA 4 HOH F 15 515 428 HOH HOH . 
CA 4 HOH F 16 516 423 HOH HOH . 
CA 4 HOH F 17 517 416 HOH HOH . 
CA 4 HOH F 18 518 425 HOH HOH . 
CA 4 HOH F 19 519 419 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 MPD . . . H 2 16.435 11.441 167.975 1 59.1 ? C1 MPD 502 A 1 
HETATM 2 C C2 MPD . . . H 2 15.011 11.2 168.466 1 59.8 ? C2 MPD 502 A 1 
HETATM 3 O O2 MPD . . . H 2 14.123 12.178 167.86 1 63.37 ? O2 MPD 502 A 1 
HETATM 4 C CM MPD . . . H 2 14.979 11.349 169.984 1 57.56 ? CM MPD 502 A 1 
HETATM 5 C C3 MPD . . . H 2 14.537 9.814 168.042 1 58.33 ? C3 MPD 502 A 1 
HETATM 6 C C4 MPD . . . H 2 13.413 9.287 168.923 1 55.13 ? C4 MPD 502 A 1 
HETATM 7 O O4 MPD . . . H 2 12.308 10.157 168.822 1 55.59 ? O4 MPD 502 A 1 
HETATM 8 C C5 MPD . . . H 2 12.998 7.892 168.472 1 53.11 ? C5 MPD 502 A 1 
#
_model_server_stats.io_time_ms              61 
_model_server_stats.parse_time_ms           37 
_model_server_stats.create_model_time_ms    24 
_model_server_stats.query_time_ms           329 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           8 
#