data_1KZU
#
_model_server_result.job_id            RkmXdeUMRdGWfhRlpl7e2g 
_model_server_result.datetime_utc      '2024-11-23 22:55:59' 
_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          1kzu 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"Q","auth_seq_id":54}' 
#
_entry.id    1KZU 
#
_exptl.entry_id    1KZU 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              715.013 
_entity.id                          3 
_entity.src_method                  man 
_entity.type                        non-polymer 
_entity.pdbx_description            'Rhodopin b-D-glucoside' 
_entity.pdbx_number_of_molecules    6 
_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         120 
_cell.entry_id            1KZU 
_cell.length_a            120.3 
_cell.length_b            120.3 
_cell.length_c            296.2 
_cell.Z_PDB               54 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1KZU 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        155 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'H 3 2' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    octadecameric 
_pdbx_struct_assembly.oligomeric_count      18 
_pdbx_struct_assembly.details               author_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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2,3 
#
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' 3_555 -x+y,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 0 0 0 
3 'crystal symmetry operation' 2_555 -y,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 0 0 0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 G N N 
? 3 J N N 
? 3 L N N 
? 3 O N N 
? 3 Q N N 
? 3 T 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 FME 1 A FME 1 1_555 A N ASN 2 A ASN 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? 
covale ? covale2 C C FME 1 D FME 1 1_555 C N ASN 2 D ASN 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? 
covale ? covale3 E C FME 1 G FME 1 1_555 E N ASN 2 G ASN 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? 
metalc ? metalc1 A O1 FME 1 A FME 1 1_555 I MG BCL . A BCL 56 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.48 ? 
metalc ? metalc2 A NE2 HIS 31 A HIS 31 1_555 H MG BCL . A BCL 55 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.354 ? 
metalc ? metalc3 B NE2 HIS 30 B HIS 30 1_555 K MG BCL . B BCL 43 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.363 ? 
metalc ? metalc4 C O1 FME 1 D FME 1 1_555 N MG BCL . D BCL 56 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.48 ? 
metalc ? metalc5 C NE2 HIS 31 D HIS 31 1_555 M MG BCL . D BCL 55 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.353 ? 
metalc ? metalc6 D NE2 HIS 30 E HIS 30 1_555 P MG BCL . E BCL 43 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.364 ? 
metalc ? metalc7 E O1 FME 1 G FME 1 1_555 S MG BCL . G BCL 56 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.48 ? 
metalc ? metalc8 E NE2 HIS 31 G HIS 31 1_555 R MG BCL . G BCL 55 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.353 ? 
metalc ? metalc9 F NE2 HIS 30 H HIS 30 1_555 U MG BCL . H BCL 43 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.363 ? 
#
_chem_comp.formula           'C46 H66 O6' 
_chem_comp.formula_weight    715.013 
_chem_comp.id                RG1 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'Rhodopin b-D-glucoside' 
_chem_comp.type              d-saccharide 
_chem_comp.pdbx_synonyms     "(3E)-3,4-didehydro-1',2'-dihydro-psi,psi-caroten-1'-yl beta-D-glucopyranoside" 
#
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
CM9 C30 RG1 sing 414 n n 
C30 CM0 RG1 sing 415 n n 
C30 C29 RG1 doub 416 n n 
C29 C28 RG1 sing 417 n n 
C28 C27 RG1 doub 418 e n 
C27 C26 RG1 sing 419 n n 
C26 CM8 RG1 sing 420 n n 
C26 C25 RG1 doub 421 e n 
C25 C24 RG1 sing 422 n n 
C24 C23 RG1 doub 423 e n 
C23 C22 RG1 sing 424 n n 
C22 C21 RG1 doub 425 e n 
C22 CM7 RG1 sing 426 n n 
C21 C20 RG1 sing 427 n n 
C20 C19 RG1 doub 428 e n 
C19 C18 RG1 sing 429 n n 
C18 C17 RG1 doub 430 e n 
C18 CM6 RG1 sing 431 n n 
C17 C16 RG1 sing 432 n n 
C16 C15 RG1 doub 433 e n 
C15 C14 RG1 sing 434 n n 
CM5 C13 RG1 sing 435 n n 
C14 C13 RG1 doub 436 e n 
C13 C12 RG1 sing 437 n n 
C12 C11 RG1 doub 438 e n 
C11 C10 RG1 sing 439 n n 
C10 C9 RG1 doub 440 e n 
CM4 C9 RG1 sing 441 n n 
C9 C8 RG1 sing 442 n n 
C8 C7 RG1 doub 443 e n 
C7 C6 RG1 sing 444 n n 
C6 C5 RG1 doub 445 e n 
CM3 C5 RG1 sing 446 n n 
C5 C4 RG1 sing 447 n n 
C4 C3 RG1 sing 448 n n 
C3 C2 RG1 sing 449 n n 
C2 C1 RG1 sing 450 n n 
CM2 C1 RG1 sing 451 n n 
CM1 C1 RG1 sing 452 n n 
C1 O1' RG1 sing 453 n n 
O1' C1' RG1 sing 454 n n 
C1' O5' RG1 sing 455 n n 
C1' C2' RG1 sing 456 n n 
O5' C5' RG1 sing 457 n n 
O2' C2' RG1 sing 458 n n 
O6' C6' RG1 sing 459 n n 
C2' C3' RG1 sing 460 n n 
C5' C6' RG1 sing 461 n n 
C5' C4' RG1 sing 462 n n 
C3' C4' RG1 sing 463 n n 
C3' O3' RG1 sing 464 n n 
C4' O4' RG1 sing 465 n n 
C1' H1 RG1 sing 466 n n 
C2' H2 RG1 sing 467 n n 
C3' H3 RG1 sing 468 n n 
C4' H4 RG1 sing 469 n n 
C5' H5 RG1 sing 470 n n 
C6' H6 RG1 sing 471 n n 
C6' H7 RG1 sing 472 n n 
O2' H8 RG1 sing 473 n n 
O3' H9 RG1 sing 474 n n 
O4' H10 RG1 sing 475 n n 
O6' H11 RG1 sing 476 n n 
CM1 H12 RG1 sing 477 n n 
CM1 H13 RG1 sing 478 n n 
CM1 H14 RG1 sing 479 n n 
CM2 H15 RG1 sing 480 n n 
CM2 H16 RG1 sing 481 n n 
CM2 H17 RG1 sing 482 n n 
C2 H18 RG1 sing 483 n n 
C2 H19 RG1 sing 484 n n 
C3 H20 RG1 sing 485 n n 
C3 H21 RG1 sing 486 n n 
C4 H22 RG1 sing 487 n n 
C4 H23 RG1 sing 488 n n 
CM3 H24 RG1 sing 489 n n 
CM3 H25 RG1 sing 490 n n 
CM3 H26 RG1 sing 491 n n 
C6 H27 RG1 sing 492 n n 
C7 H28 RG1 sing 493 n n 
C8 H29 RG1 sing 494 n n 
CM4 H30 RG1 sing 495 n n 
CM4 H31 RG1 sing 496 n n 
CM4 H32 RG1 sing 497 n n 
C10 H33 RG1 sing 498 n n 
C11 H34 RG1 sing 499 n n 
C12 H35 RG1 sing 500 n n 
CM5 H36 RG1 sing 501 n n 
CM5 H37 RG1 sing 502 n n 
CM5 H38 RG1 sing 503 n n 
C14 H39 RG1 sing 504 n n 
C15 H40 RG1 sing 505 n n 
C16 H41 RG1 sing 506 n n 
C17 H42 RG1 sing 507 n n 
CM6 H43 RG1 sing 508 n n 
CM6 H44 RG1 sing 509 n n 
CM6 H45 RG1 sing 510 n n 
C19 H46 RG1 sing 511 n n 
C20 H47 RG1 sing 512 n n 
C21 H48 RG1 sing 513 n n 
CM7 H49 RG1 sing 514 n n 
CM7 H50 RG1 sing 515 n n 
CM7 H51 RG1 sing 516 n n 
C23 H52 RG1 sing 517 n n 
C24 H53 RG1 sing 518 n n 
C25 H54 RG1 sing 519 n n 
CM8 H55 RG1 sing 520 n n 
CM8 H56 RG1 sing 521 n n 
CM8 H57 RG1 sing 522 n n 
C27 H58 RG1 sing 523 n n 
C28 H59 RG1 sing 524 n n 
C29 H60 RG1 sing 525 n n 
CM9 H61 RG1 sing 526 n n 
CM9 H62 RG1 sing 527 n n 
CM9 H63 RG1 sing 528 n n 
CM0 H64 RG1 sing 529 n n 
CM0 H65 RG1 sing 530 n n 
CM0 H66 RG1 sing 531 n n 
#
_atom_sites.entry_id                     1KZU 
_atom_sites.fract_transf_matrix[1][1]    0.008313 
_atom_sites.fract_transf_matrix[1][2]    0.004799 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.009599 
_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]    0.003376 
_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 3 RG1 A 1 54 13 RG1 RG1 . 
H 4 BCL A 1 55 1 BCL BCL . 
I 4 BCL A 1 56 7 BCL BCL . 
J 3 RG1 B 1 42 10 RG1 RG1 . 
K 4 BCL B 1 43 2 BCL BCL . 
L 3 RG1 D 1 54 13 RG1 RG1 . 
M 4 BCL D 1 55 1 BCL BCL . 
N 4 BCL D 1 56 7 BCL BCL . 
O 3 RG1 E 1 42 10 RG1 RG1 . 
P 4 BCL E 1 43 2 BCL BCL . 
Q 3 RG1 G 1 54 13 RG1 RG1 . 
R 4 BCL G 1 55 1 BCL BCL . 
S 4 BCL G 1 56 7 BCL BCL . 
T 3 RG1 H 1 42 10 RG1 RG1 . 
U 4 BCL H 1 43 2 BCL BCL . 
V 5 HOH A 1 57 1 HOH HOH . 
V 5 HOH A 2 58 4 HOH HOH . 
V 5 HOH A 3 59 7 HOH HOH . 
V 5 HOH A 4 60 8 HOH HOH . 
V 5 HOH A 5 61 9 HOH HOH . 
V 5 HOH A 6 62 10 HOH HOH . 
V 5 HOH A 7 63 11 HOH HOH . 
V 5 HOH A 8 64 12 HOH HOH . 
V 5 HOH A 9 65 15 HOH HOH . 
V 5 HOH A 10 66 16 HOH HOH . 
V 5 HOH A 11 67 17 HOH HOH . 
W 5 HOH B 1 44 3 HOH HOH . 
W 5 HOH B 2 45 6 HOH HOH . 
W 5 HOH B 3 46 13 HOH HOH . 
W 5 HOH B 4 47 14 HOH HOH . 
X 5 HOH D 1 57 1 HOH HOH . 
X 5 HOH D 2 58 4 HOH HOH . 
X 5 HOH D 3 59 7 HOH HOH . 
X 5 HOH D 4 60 8 HOH HOH . 
X 5 HOH D 5 61 9 HOH HOH . 
X 5 HOH D 6 62 10 HOH HOH . 
X 5 HOH D 7 63 11 HOH HOH . 
X 5 HOH D 8 64 12 HOH HOH . 
X 5 HOH D 9 65 15 HOH HOH . 
X 5 HOH D 10 66 16 HOH HOH . 
X 5 HOH D 11 67 17 HOH HOH . 
Y 5 HOH E 1 44 2 HOH HOH . 
Y 5 HOH E 2 45 5 HOH HOH . 
Y 5 HOH E 3 46 3 HOH HOH . 
Y 5 HOH E 4 47 6 HOH HOH . 
Y 5 HOH E 5 48 13 HOH HOH . 
Y 5 HOH E 6 49 14 HOH HOH . 
Z 5 HOH G 1 57 1 HOH HOH . 
Z 5 HOH G 2 58 2 HOH HOH . 
Z 5 HOH G 3 59 4 HOH HOH . 
Z 5 HOH G 4 60 5 HOH HOH . 
Z 5 HOH G 5 61 7 HOH HOH . 
Z 5 HOH G 6 62 8 HOH HOH . 
Z 5 HOH G 7 63 9 HOH HOH . 
Z 5 HOH G 8 64 10 HOH HOH . 
Z 5 HOH G 9 65 11 HOH HOH . 
Z 5 HOH G 10 66 12 HOH HOH . 
Z 5 HOH G 11 67 15 HOH HOH . 
Z 5 HOH G 12 68 16 HOH HOH . 
Z 5 HOH G 13 69 17 HOH HOH . 
AA 5 HOH H 1 44 2 HOH HOH . 
AA 5 HOH H 2 45 5 HOH HOH . 
AA 5 HOH H 3 46 3 HOH HOH . 
AA 5 HOH H 4 47 6 HOH HOH . 
AA 5 HOH H 5 48 13 HOH HOH . 
AA 5 HOH H 6 49 14 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' RG1 . . . Q 3 12.163 28.978 11.658 0.5 54.89 ? C1' RG1 54 G 1 
HETATM 2 C C2' RG1 . . . Q 3 12.244 28.117 10.394 0.5 57.04 ? C2' RG1 54 G 1 
HETATM 3 C C3' RG1 . . . Q 3 13.666 28.07 9.808 0.5 60.66 ? C3' RG1 54 G 1 
HETATM 4 C C4' RG1 . . . Q 3 14.325 29.459 9.805 0.5 62.39 ? C4' RG1 54 G 1 
HETATM 5 C C5' RG1 . . . Q 3 14.236 30.102 11.192 0.5 62.04 ? C5' RG1 54 G 1 
HETATM 6 C C6' RG1 . . . Q 3 14.881 31.507 11.189 0.5 63.6 ? C6' RG1 54 G 1 
HETATM 7 O O1' RG1 . . . Q 3 12.457 28.272 12.87 0.5 49.9 ? O1' RG1 54 G 1 
HETATM 8 O O2' RG1 . . . Q 3 11.796 26.809 10.676 0.5 59.41 ? O2' RG1 54 G 1 
HETATM 9 O O3' RG1 . . . Q 3 13.611 27.569 8.475 0.5 62.86 ? O3' RG1 54 G 1 
HETATM 10 O O4' RG1 . . . Q 3 15.691 29.371 9.396 0.5 60.31 ? O4' RG1 54 G 1 
HETATM 11 O O5' RG1 . . . Q 3 12.861 30.212 11.541 0.5 60.47 ? O5' RG1 54 G 1 
HETATM 12 O O6' RG1 . . . Q 3 14.102 32.481 11.89 0.5 63.36 ? O6' RG1 54 G 1 
HETATM 13 C C1 RG1 . . . Q 3 11.634 28.744 13.951 1 47.78 ? C1 RG1 54 G 1 
HETATM 14 C CM1 RG1 . . . Q 3 10.184 28.514 13.601 1 53.25 ? CM1 RG1 54 G 1 
HETATM 15 C CM2 RG1 . . . Q 3 11.866 30.206 14.15 1 58 ? CM2 RG1 54 G 1 
HETATM 16 C C2 RG1 . . . Q 3 11.966 28.011 15.288 1 44.09 ? C2 RG1 54 G 1 
HETATM 17 C C3 RG1 . . . Q 3 10.841 28.259 16.293 1 28.2 ? C3 RG1 54 G 1 
HETATM 18 C C4 RG1 . . . Q 3 11.311 28.994 17.521 1 37.02 ? C4 RG1 54 G 1 
HETATM 19 C C5 RG1 . . . Q 3 11.656 28.046 18.631 1 31.54 ? C5 RG1 54 G 1 
HETATM 20 C CM3 RG1 . . . Q 3 12.355 26.792 18.327 1 39.86 ? CM3 RG1 54 G 1 
HETATM 21 C C6 RG1 . . . Q 3 11.504 28.435 19.938 1 37.17 ? C6 RG1 54 G 1 
HETATM 22 C C7 RG1 . . . Q 3 12.375 27.987 20.904 1 34.73 ? C7 RG1 54 G 1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    14 
_model_server_stats.query_time_ms           337 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           22 
#