data_1KHR
#
_model_server_result.job_id            iYPnrUZ5caU1ITo8mTPcCQ 
_model_server_result.datetime_utc      '2024-12-01 18:02:01' 
_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          1khr 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"G","auth_seq_id":401}' 
#
_entry.id    1KHR 
#
_exptl.entry_id    1KHR 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              525.593 
_entity.id                          2 
_entity.src_method                  nat 
_entity.type                        non-polymer 
_entity.pdbx_description            'VIRGINIAMYCIN M1' 
_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          90 
_cell.angle_gamma         90 
_cell.entry_id            1KHR 
_cell.length_a            186.1 
_cell.length_b            185.9 
_cell.length_c            186.9 
_cell.Z_PDB               96 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1KHR 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        22 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'F 2 2 2' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA trimeric 3 author_and_software_defined_assembly 1 
PISA trimeric 3 author_and_software_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,C,G,H,I,J,K,P,Q,R 1 1 
D,E,F,L,M,N,O,S,T,U 2 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 M N N 
#
_chem_comp.formula           'C28 H35 N3 O7' 
_chem_comp.formula_weight    525.593 
_chem_comp.id                VIR 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'VIRGINIAMYCIN M1' 
_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 VIR doub 462 n n 
C1 C37 VIR sing 463 n n 
C1 N5 VIR sing 464 n n 
C10 C13 VIR sing 465 n n 
C10 N9 VIR doub 466 n y 
C10 O11 VIR sing 467 n y 
C12 C8 VIR doub 468 n y 
C12 O11 VIR sing 469 n y 
C12 H12 VIR sing 470 n n 
C13 C14 VIR sing 471 n n 
C13 H131 VIR sing 472 n n 
C13 H132 VIR sing 473 n n 
C14 C16 VIR sing 474 n n 
C14 O15 VIR doub 475 n n 
C16 C17 VIR sing 476 n n 
C16 H161 VIR sing 477 n n 
C16 H162 VIR sing 478 n n 
C17 C19 VIR sing 479 n n 
C17 O18 VIR sing 480 n n 
C17 H17 VIR sing 481 n n 
C19 C20 VIR doub 482 e n 
C19 H19 VIR sing 483 n n 
C2 C3 VIR sing 484 n n 
C2 HC2 VIR sing 485 n n 
C20 C21 VIR sing 486 n n 
C20 C22 VIR sing 487 n n 
C21 H211 VIR sing 488 n n 
C21 H212 VIR sing 489 n n 
C21 H213 VIR sing 490 n n 
C22 C23 VIR doub 491 e n 
C22 H22 VIR sing 492 n n 
C23 C24 VIR sing 493 n n 
C23 H23 VIR sing 494 n n 
C24 N25 VIR sing 495 n n 
C24 H241 VIR sing 496 n n 
C24 H242 VIR sing 497 n n 
C26 C28 VIR sing 498 n n 
C26 N25 VIR sing 499 n n 
C26 O27 VIR doub 500 n n 
C28 C29 VIR doub 501 e n 
C28 H28 VIR sing 502 n n 
C29 C30 VIR sing 503 n n 
C29 H29 VIR sing 504 n n 
C3 C4 VIR sing 505 n n 
C3 HC31 VIR sing 506 n n 
C3 HC32 VIR sing 507 n n 
C30 C31 VIR sing 508 n n 
C30 C32 VIR sing 509 n n 
C30 H30 VIR sing 510 n n 
C31 H311 VIR sing 511 n n 
C31 H312 VIR sing 512 n n 
C31 H313 VIR sing 513 n n 
C32 C33 VIR sing 514 n n 
C32 O36 VIR sing 515 n n 
C32 H32 VIR sing 516 n n 
C33 C34 VIR sing 517 n n 
C33 C35 VIR sing 518 n n 
C33 H33 VIR sing 519 n n 
C34 H341 VIR sing 520 n n 
C34 H342 VIR sing 521 n n 
C34 H343 VIR sing 522 n n 
C35 H351 VIR sing 523 n n 
C35 H352 VIR sing 524 n n 
C35 H353 VIR sing 525 n n 
C37 O36 VIR sing 526 n n 
C37 O38 VIR doub 527 n n 
C4 N5 VIR sing 528 n n 
C4 HC41 VIR sing 529 n n 
C4 HC42 VIR sing 530 n n 
C6 C8 VIR sing 531 n n 
C6 N5 VIR sing 532 n n 
C6 O7 VIR doub 533 n n 
C8 N9 VIR sing 534 n y 
N25 H25 VIR sing 535 n n 
O18 H18' VIR sing 536 n n 
#
_atom_sites.entry_id                     1KHR 
_atom_sites.fract_transf_matrix[1][1]    0.005373 
_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]    0.005379 
_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]    0.00535 
_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 VIR A 1 401 305 VIR VIR . 
H 2 VIR A 1 402 305 VIR VIR . 
I 3 COA A 1 301 302 COA COA . 
J 3 COA B 1 302 302 COA COA . 
K 3 COA C 1 303 302 COA COA . 
L 3 COA D 1 304 302 COA COA . 
M 2 VIR E 1 403 305 VIR VIR . 
N 3 COA E 1 305 302 COA COA . 
O 3 COA F 1 306 302 COA COA . 
P 4 HOH A 1 3514 3514 HOH TIP . 
P 4 HOH A 2 3519 3519 HOH TIP . 
P 4 HOH A 3 3520 3520 HOH TIP . 
P 4 HOH A 4 3523 3523 HOH TIP . 
P 4 HOH A 5 3526 3526 HOH TIP . 
P 4 HOH A 6 3533 3533 HOH TIP . 
P 4 HOH A 7 3550 3550 HOH TIP . 
P 4 HOH A 8 3559 3559 HOH TIP . 
P 4 HOH A 9 3583 3583 HOH TIP . 
P 4 HOH A 10 3584 3584 HOH TIP . 
P 4 HOH A 11 3603 3603 HOH TIP . 
P 4 HOH A 12 3607 3607 HOH TIP . 
P 4 HOH A 13 3608 3608 HOH TIP . 
P 4 HOH A 14 3611 3611 HOH TIP . 
P 4 HOH A 15 3623 3623 HOH TIP . 
Q 4 HOH B 1 3500 3500 HOH TIP . 
Q 4 HOH B 2 3503 3503 HOH TIP . 
Q 4 HOH B 3 3504 3504 HOH TIP . 
Q 4 HOH B 4 3505 3505 HOH TIP . 
Q 4 HOH B 5 3506 3506 HOH TIP . 
Q 4 HOH B 6 3507 3507 HOH TIP . 
Q 4 HOH B 7 3508 3508 HOH TIP . 
Q 4 HOH B 8 3511 3511 HOH TIP . 
Q 4 HOH B 9 3534 3534 HOH TIP . 
Q 4 HOH B 10 3542 3542 HOH TIP . 
Q 4 HOH B 11 3544 3544 HOH TIP . 
Q 4 HOH B 12 3546 3546 HOH TIP . 
Q 4 HOH B 13 3549 3549 HOH TIP . 
Q 4 HOH B 14 3563 3563 HOH TIP . 
Q 4 HOH B 15 3568 3568 HOH TIP . 
Q 4 HOH B 16 3572 3572 HOH TIP . 
Q 4 HOH B 17 3576 3576 HOH TIP . 
Q 4 HOH B 18 3577 3577 HOH TIP . 
Q 4 HOH B 19 3578 3578 HOH TIP . 
Q 4 HOH B 20 3579 3579 HOH TIP . 
Q 4 HOH B 21 3585 3585 HOH TIP . 
Q 4 HOH B 22 3612 3612 HOH TIP . 
R 4 HOH C 1 3517 3517 HOH TIP . 
R 4 HOH C 2 3521 3521 HOH TIP . 
R 4 HOH C 3 3527 3527 HOH TIP . 
R 4 HOH C 4 3530 3530 HOH TIP . 
R 4 HOH C 5 3532 3532 HOH TIP . 
R 4 HOH C 6 3535 3535 HOH TIP . 
R 4 HOH C 7 3543 3543 HOH TIP . 
R 4 HOH C 8 3552 3552 HOH TIP . 
R 4 HOH C 9 3561 3561 HOH TIP . 
R 4 HOH C 10 3573 3573 HOH TIP . 
R 4 HOH C 11 3582 3582 HOH TIP . 
R 4 HOH C 12 3586 3586 HOH TIP . 
R 4 HOH C 13 3587 3587 HOH TIP . 
R 4 HOH C 14 3604 3604 HOH TIP . 
R 4 HOH C 15 3605 3605 HOH TIP . 
R 4 HOH C 16 3606 3606 HOH TIP . 
S 4 HOH D 1 3502 3502 HOH TIP . 
S 4 HOH D 2 3512 3512 HOH TIP . 
S 4 HOH D 3 3513 3513 HOH TIP . 
S 4 HOH D 4 3524 3524 HOH TIP . 
S 4 HOH D 5 3528 3528 HOH TIP . 
S 4 HOH D 6 3529 3529 HOH TIP . 
S 4 HOH D 7 3531 3531 HOH TIP . 
S 4 HOH D 8 3538 3538 HOH TIP . 
S 4 HOH D 9 3540 3540 HOH TIP . 
S 4 HOH D 10 3541 3541 HOH TIP . 
S 4 HOH D 11 3548 3548 HOH TIP . 
S 4 HOH D 12 3551 3551 HOH TIP . 
S 4 HOH D 13 3553 3553 HOH TIP . 
S 4 HOH D 14 3555 3555 HOH TIP . 
S 4 HOH D 15 3569 3569 HOH TIP . 
S 4 HOH D 16 3571 3571 HOH TIP . 
S 4 HOH D 17 3580 3580 HOH TIP . 
S 4 HOH D 18 3588 3588 HOH TIP . 
S 4 HOH D 19 3590 3590 HOH TIP . 
S 4 HOH D 20 3591 3591 HOH TIP . 
S 4 HOH D 21 3592 3592 HOH TIP . 
S 4 HOH D 22 3614 3614 HOH TIP . 
S 4 HOH D 23 3620 3620 HOH TIP . 
T 4 HOH E 1 3509 3509 HOH TIP . 
T 4 HOH E 2 3510 3510 HOH TIP . 
T 4 HOH E 3 3515 3515 HOH TIP . 
T 4 HOH E 4 3518 3518 HOH TIP . 
T 4 HOH E 5 3525 3525 HOH TIP . 
T 4 HOH E 6 3537 3537 HOH TIP . 
T 4 HOH E 7 3539 3539 HOH TIP . 
T 4 HOH E 8 3547 3547 HOH TIP . 
T 4 HOH E 9 3554 3554 HOH TIP . 
T 4 HOH E 10 3557 3557 HOH TIP . 
T 4 HOH E 11 3558 3558 HOH TIP . 
T 4 HOH E 12 3564 3564 HOH TIP . 
T 4 HOH E 13 3565 3565 HOH TIP . 
T 4 HOH E 14 3567 3567 HOH TIP . 
T 4 HOH E 15 3570 3570 HOH TIP . 
T 4 HOH E 16 3574 3574 HOH TIP . 
T 4 HOH E 17 3593 3593 HOH TIP . 
T 4 HOH E 18 3594 3594 HOH TIP . 
T 4 HOH E 19 3595 3595 HOH TIP . 
T 4 HOH E 20 3596 3596 HOH TIP . 
T 4 HOH E 21 3615 3615 HOH TIP . 
T 4 HOH E 22 3616 3616 HOH TIP . 
T 4 HOH E 23 3622 3622 HOH TIP . 
U 4 HOH F 1 3501 3501 HOH TIP . 
U 4 HOH F 2 3516 3516 HOH TIP . 
U 4 HOH F 3 3522 3522 HOH TIP . 
U 4 HOH F 4 3536 3536 HOH TIP . 
U 4 HOH F 5 3545 3545 HOH TIP . 
U 4 HOH F 6 3562 3562 HOH TIP . 
U 4 HOH F 7 3566 3566 HOH TIP . 
U 4 HOH F 8 3598 3598 HOH TIP . 
U 4 HOH F 9 3599 3599 HOH TIP . 
U 4 HOH F 10 3600 3600 HOH TIP . 
U 4 HOH F 11 3602 3602 HOH TIP . 
U 4 HOH F 12 3619 3619 HOH TIP . 
U 4 HOH F 13 3621 3621 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
HETATM 1 C C1 VIR . . . G 2 66.198 7.922 41.108 0.8 31.61 ? C1 VIR 401 A 1 
HETATM 2 C C10 VIR . . . G 2 62.531 11.569 39.014 0.8 39.69 ? C10 VIR 401 A 1 
HETATM 3 C C12 VIR . . . G 2 62.786 11.451 41.169 0.8 37.76 ? C12 VIR 401 A 1 
HETATM 4 C C13 VIR . . . G 2 61.995 12.179 37.775 0.8 44.8 ? C13 VIR 401 A 1 
HETATM 5 C C14 VIR . . . G 2 62.689 11.735 36.558 0.8 49.21 ? C14 VIR 401 A 1 
HETATM 6 C C16 VIR . . . G 2 62.381 10.39 35.97 0.8 43.79 ? C16 VIR 401 A 1 
HETATM 7 C C17 VIR . . . G 2 63.531 9.831 35.167 0.8 34.88 ? C17 VIR 401 A 1 
HETATM 8 C C19 VIR . . . G 2 63.968 8.456 35.616 0.8 32.83 ? C19 VIR 401 A 1 
HETATM 9 C C2 VIR . . . G 2 67.377 7.978 40.453 0.8 30.42 ? C2 VIR 401 A 1 
HETATM 10 C C20 VIR . . . G 2 65.184 8.003 35.568 0.8 27.45 ? C20 VIR 401 A 1 
HETATM 11 C C21 VIR . . . G 2 66.341 8.82 35.046 0.8 26.32 ? C21 VIR 401 A 1 
HETATM 12 C C22 VIR . . . G 2 65.472 6.687 36.059 0.8 22.19 ? C22 VIR 401 A 1 
HETATM 13 C C23 VIR . . . G 2 66.78 6.303 36.199 0.8 22.87 ? C23 VIR 401 A 1 
HETATM 14 C C24 VIR . . . G 2 67.221 4.932 36.761 0.8 23.2 ? C24 VIR 401 A 1 
HETATM 15 C C26 VIR . . . G 2 67.03 4.132 39.034 0.8 28.86 ? C26 VIR 401 A 1 
HETATM 16 C C28 VIR . . . G 2 67.659 4.726 40.334 0.8 29.71 ? C28 VIR 401 A 1 
HETATM 17 C C29 VIR . . . G 2 67.604 4.083 41.257 0.8 30.15 ? C29 VIR 401 A 1 
HETATM 18 C C3 VIR . . . G 2 67.366 9.071 39.442 0.8 28.68 ? C3 VIR 401 A 1 
HETATM 19 C C30 VIR . . . G 2 68.073 4.194 42.741 0.8 29.27 ? C30 VIR 401 A 1 
HETATM 20 C C31 VIR . . . G 2 69.591 4.381 42.909 0.8 28.96 ? C31 VIR 401 A 1 
HETATM 21 C C32 VIR . . . G 2 67.287 5.343 43.407 0.8 30.46 ? C32 VIR 401 A 1 
HETATM 22 C C33 VIR . . . G 2 68.01 5.898 44.602 0.8 31.16 ? C33 VIR 401 A 1 
HETATM 23 C C34 VIR . . . G 2 67.193 7.034 45.234 0.8 28.03 ? C34 VIR 401 A 1 
HETATM 24 C C35 VIR . . . G 2 68.212 4.789 45.65 0.8 30.98 ? C35 VIR 401 A 1 
HETATM 25 C C37 VIR . . . G 2 65.932 6.861 42.115 0.8 31.24 ? C37 VIR 401 A 1 
HETATM 26 C C4 VIR . . . G 2 65.987 9.681 39.532 0.8 30.02 ? C4 VIR 401 A 1 
HETATM 27 C C6 VIR . . . G 2 64.233 9.415 41.315 0.8 34.05 ? C6 VIR 401 A 1 
HETATM 28 C C8 VIR . . . G 2 63.463 10.432 40.571 0.8 37.66 ? C8 VIR 401 A 1 
HETATM 29 N N25 VIR . . . G 2 67.522 5.013 38.165 0.8 25.8 ? N25 VIR 401 A 1 
HETATM 30 N N5 VIR . . . G 2 65.285 8.923 40.63 0.8 30.72 ? N5 VIR 401 A 1 
HETATM 31 N N9 VIR . . . G 2 63.287 10.52 39.196 0.8 37.9 ? N9 VIR 401 A 1 
HETATM 32 O O11 VIR . . . G 2 62.182 12.18 40.194 0.8 37.63 ? O11 VIR 401 A 1 
HETATM 33 O O15 VIR . . . G 2 63.502 12.502 36.043 0.8 52 ? O15 VIR 401 A 1 
HETATM 34 O O18 VIR . . . G 2 63.094 9.724 33.775 0.8 37.91 ? O18 VIR 401 A 1 
HETATM 35 O O27 VIR . . . G 2 66.265 3.189 38.729 0.8 27.8 ? O27 VIR 401 A 1 
HETATM 36 O O36 VIR . . . G 2 67.173 6.462 42.478 0.8 32.42 ? O36 VIR 401 A 1 
HETATM 37 O O38 VIR . . . G 2 64.896 6.393 42.539 0.8 33.6 ? O38 VIR 401 A 1 
HETATM 38 O O7 VIR . . . G 2 63.909 9.097 42.459 0.8 35.37 ? O7 VIR 401 A 1 
#
_model_server_stats.io_time_ms              39 
_model_server_stats.parse_time_ms           26 
_model_server_stats.create_model_time_ms    82 
_model_server_stats.query_time_ms           1309 
_model_server_stats.encode_time_ms          17 
_model_server_stats.element_count           38 
#