data_6YBH
#
_model_server_result.job_id            ju8XwmjXGXEKi1iOsSWpYA 
_model_server_result.datetime_utc      '2024-11-15 05:40:08' 
_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          6ybh 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"V","auth_seq_id":301}' 
#
_entry.id    6YBH 
#
_exptl.entry_id    6YBH 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              265.265 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            Pyrrolo-dC 
_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            6YBH 
_cell.length_a            190.929 
_cell.length_b            190.929 
_cell.length_c            115.461 
_cell.Z_PDB               54 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6YBH 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        146 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'H 3' 
#
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 dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 author_and_software_defined_assembly 2 
PISA dimeric 2 author_and_software_defined_assembly 3 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,G,H,I,J,K,L,M,N,O,V,W,X,Y,Z,SA,UA 1 1 
B,D,P,Q,R,S,T,U,AA,BA,CA,DA,EA,FA,GA,TA,VA 2 1 
E,F,HA,IA,JA,KA,LA,MA,NA,OA,PA,QA,RA,WA,XA 3 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 P N N 
? 2 V N N 
? 2 AA N N 
? 2 HA N N 
? 2 OA N N 
#
_chem_comp.formula           'C12 H15 N3 O4' 
_chem_comp.formula_weight    265.265 
_chem_comp.id                8LK 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              Pyrrolo-dC 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     "3-[(2R,4S,5R)-(hydroxymethyl)-4-oxidanyl-oxolan-2-yl]-6-methyl-7H-pyrrolo[2,3-d]pyrimidin-2-one;6-Methyl-3-(beta-D-2-deoxyribofuranosyl)pyrrolo[2,3-d]pyrimidin-2-one;N-Pyrrolo-2'-deoxycytidine" 
#
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
N17 C15 8LK sing 1 n n 
N17 C4 8LK sing 2 n n 
C16 C15 8LK sing 3 n n 
N3 C4 8LK doub 4 n n 
N3 C2 8LK sing 5 n n 
C15 C14 8LK doub 6 n n 
C4 C5 8LK sing 7 n n 
O2 C2 8LK doub 8 n n 
C2 N1 8LK sing 9 n n 
C14 C5 8LK sing 10 n n 
C5 C6 8LK doub 11 n n 
N1 C6 8LK sing 12 n n 
N1 C1' 8LK sing 13 n n 
C2' C1' 8LK sing 14 n n 
C2' C3' 8LK sing 15 n n 
C1' O4' 8LK sing 16 n n 
C3' O3' 8LK sing 17 n n 
C3' C4' 8LK sing 18 n n 
O5' C5' 8LK sing 19 n n 
O4' C4' 8LK sing 20 n n 
C4' C5' 8LK sing 21 n n 
O5' H1 8LK sing 22 n n 
C5' H2 8LK sing 23 n n 
C5' H3 8LK sing 24 n n 
C4' H4 8LK sing 25 n n 
C3' H5 8LK sing 26 n n 
O3' H6 8LK sing 27 n n 
C2' H7 8LK sing 28 n n 
C2' H8 8LK sing 29 n n 
C1' H9 8LK sing 30 n n 
C14 H13 8LK sing 31 n n 
C16 H14 8LK sing 32 n n 
C16 H15 8LK sing 33 n n 
C16 H16 8LK sing 34 n n 
N17 H17 8LK sing 35 n n 
C6 H10 8LK sing 36 n n 
#
_atom_sites.entry_id                     6YBH 
_atom_sites.fract_transf_matrix[1][1]    0.005238 
_atom_sites.fract_transf_matrix[1][2]    0.003024 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.006048 
_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]    0.008661 
_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 8LK A 1 301 515 8LK 4PC . 
H 3 SO4 A 1 302 7 SO4 SO4 . 
I 3 SO4 A 1 303 16 SO4 SO4 . 
J 3 SO4 A 1 304 21 SO4 SO4 . 
K 3 SO4 A 1 305 25 SO4 SO4 . 
L 3 SO4 A 1 306 27 SO4 SO4 . 
M 3 SO4 A 1 307 33 SO4 SO4 . 
N 4 GOL A 1 308 9 GOL GOL . 
O 4 GOL A 1 309 12 GOL GOL . 
P 2 8LK B 1 301 515 8LK 4PC . 
Q 3 SO4 B 1 302 5 SO4 SO4 . 
R 3 SO4 B 1 303 9 SO4 SO4 . 
S 3 SO4 B 1 304 24 SO4 SO4 . 
T 3 SO4 B 1 305 29 SO4 SO4 . 
U 4 GOL B 1 306 2 GOL GOL . 
V 2 8LK C 1 301 515 8LK 4PC . 
W 3 SO4 C 1 302 2 SO4 SO4 . 
X 3 SO4 C 1 303 11 SO4 SO4 . 
Y 3 SO4 C 1 304 15 SO4 SO4 . 
Z 4 GOL C 1 305 6 GOL GOL . 
AA 2 8LK D 1 301 515 8LK 4PC . 
BA 3 SO4 D 1 302 6 SO4 SO4 . 
CA 3 SO4 D 1 303 30 SO4 SO4 . 
DA 3 SO4 D 1 304 32 SO4 SO4 . 
EA 4 GOL D 1 305 1 GOL GOL . 
FA 4 GOL D 1 306 4 GOL GOL . 
GA 4 GOL D 1 307 7 GOL GOL . 
HA 2 8LK E 1 301 515 8LK 4PC . 
IA 3 SO4 E 1 302 18 SO4 SO4 . 
JA 3 SO4 E 1 303 28 SO4 SO4 . 
KA 3 SO4 E 1 304 34 SO4 SO4 . 
LA 4 GOL E 1 305 5 GOL GOL . 
MA 4 GOL E 1 306 8 GOL GOL . 
NA 4 GOL E 1 307 10 GOL GOL . 
OA 2 8LK F 1 301 515 8LK 4PC . 
PA 3 SO4 F 1 302 1 SO4 SO4 . 
QA 3 SO4 F 1 303 13 SO4 SO4 . 
RA 4 GOL F 1 304 11 GOL GOL . 
SA 5 HOH A 1 401 37 HOH HOH . 
SA 5 HOH A 2 402 85 HOH HOH . 
SA 5 HOH A 3 403 4 HOH HOH . 
SA 5 HOH A 4 404 59 HOH HOH . 
SA 5 HOH A 5 405 41 HOH HOH . 
SA 5 HOH A 6 406 60 HOH HOH . 
SA 5 HOH A 7 407 11 HOH HOH . 
SA 5 HOH A 8 408 94 HOH HOH . 
SA 5 HOH A 9 409 1 HOH HOH . 
SA 5 HOH A 10 410 31 HOH HOH . 
SA 5 HOH A 11 411 44 HOH HOH . 
SA 5 HOH A 12 412 6 HOH HOH . 
SA 5 HOH A 13 413 61 HOH HOH . 
SA 5 HOH A 14 414 23 HOH HOH . 
SA 5 HOH A 15 415 50 HOH HOH . 
SA 5 HOH A 16 416 72 HOH HOH . 
SA 5 HOH A 17 417 62 HOH HOH . 
SA 5 HOH A 18 418 54 HOH HOH . 
SA 5 HOH A 19 419 86 HOH HOH . 
SA 5 HOH A 20 420 28 HOH HOH . 
SA 5 HOH A 21 421 92 HOH HOH . 
SA 5 HOH A 22 422 83 HOH HOH . 
SA 5 HOH A 23 423 57 HOH HOH . 
TA 5 HOH B 1 401 75 HOH HOH . 
TA 5 HOH B 2 402 74 HOH HOH . 
TA 5 HOH B 3 403 12 HOH HOH . 
TA 5 HOH B 4 404 77 HOH HOH . 
TA 5 HOH B 5 405 67 HOH HOH . 
TA 5 HOH B 6 406 22 HOH HOH . 
TA 5 HOH B 7 407 18 HOH HOH . 
TA 5 HOH B 8 408 47 HOH HOH . 
TA 5 HOH B 9 409 2 HOH HOH . 
TA 5 HOH B 10 410 5 HOH HOH . 
TA 5 HOH B 11 411 63 HOH HOH . 
TA 5 HOH B 12 412 42 HOH HOH . 
TA 5 HOH B 13 413 27 HOH HOH . 
TA 5 HOH B 14 414 13 HOH HOH . 
TA 5 HOH B 15 415 45 HOH HOH . 
TA 5 HOH B 16 416 76 HOH HOH . 
TA 5 HOH B 17 417 87 HOH HOH . 
TA 5 HOH B 18 418 95 HOH HOH . 
TA 5 HOH B 19 419 91 HOH HOH . 
TA 5 HOH B 20 420 65 HOH HOH . 
UA 5 HOH C 1 401 17 HOH HOH . 
UA 5 HOH C 2 402 52 HOH HOH . 
UA 5 HOH C 3 403 53 HOH HOH . 
UA 5 HOH C 4 404 3 HOH HOH . 
UA 5 HOH C 5 405 51 HOH HOH . 
UA 5 HOH C 6 406 48 HOH HOH . 
UA 5 HOH C 7 407 7 HOH HOH . 
UA 5 HOH C 8 408 9 HOH HOH . 
UA 5 HOH C 9 409 33 HOH HOH . 
UA 5 HOH C 10 410 100 HOH HOH . 
UA 5 HOH C 11 411 30 HOH HOH . 
UA 5 HOH C 12 412 81 HOH HOH . 
UA 5 HOH C 13 413 88 HOH HOH . 
UA 5 HOH C 14 414 8 HOH HOH . 
UA 5 HOH C 15 415 66 HOH HOH . 
UA 5 HOH C 16 416 71 HOH HOH . 
UA 5 HOH C 17 417 49 HOH HOH . 
UA 5 HOH C 18 418 32 HOH HOH . 
UA 5 HOH C 19 419 70 HOH HOH . 
UA 5 HOH C 20 420 43 HOH HOH . 
UA 5 HOH C 21 421 73 HOH HOH . 
UA 5 HOH C 22 422 69 HOH HOH . 
UA 5 HOH C 23 423 96 HOH HOH . 
VA 5 HOH D 1 401 10 HOH HOH . 
VA 5 HOH D 2 402 84 HOH HOH . 
VA 5 HOH D 3 403 14 HOH HOH . 
VA 5 HOH D 4 404 24 HOH HOH . 
VA 5 HOH D 5 405 68 HOH HOH . 
VA 5 HOH D 6 406 38 HOH HOH . 
VA 5 HOH D 7 407 80 HOH HOH . 
VA 5 HOH D 8 408 26 HOH HOH . 
VA 5 HOH D 9 409 97 HOH HOH . 
VA 5 HOH D 10 410 25 HOH HOH . 
VA 5 HOH D 11 411 34 HOH HOH . 
VA 5 HOH D 12 412 58 HOH HOH . 
VA 5 HOH D 13 413 19 HOH HOH . 
VA 5 HOH D 14 414 36 HOH HOH . 
VA 5 HOH D 15 415 103 HOH HOH . 
WA 5 HOH E 1 401 16 HOH HOH . 
WA 5 HOH E 2 402 21 HOH HOH . 
WA 5 HOH E 3 403 93 HOH HOH . 
WA 5 HOH E 4 404 39 HOH HOH . 
WA 5 HOH E 5 405 29 HOH HOH . 
WA 5 HOH E 6 406 55 HOH HOH . 
WA 5 HOH E 7 407 64 HOH HOH . 
WA 5 HOH E 8 408 35 HOH HOH . 
WA 5 HOH E 9 409 46 HOH HOH . 
WA 5 HOH E 10 410 82 HOH HOH . 
WA 5 HOH E 11 411 90 HOH HOH . 
XA 5 HOH F 1 401 79 HOH HOH . 
XA 5 HOH F 2 402 56 HOH HOH . 
XA 5 HOH F 3 403 20 HOH HOH . 
XA 5 HOH F 4 404 102 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 O O5' 8LK . . . V 2 74.441 -17.45 -28.398 1 60.61 ? O5' 8LK 301 C 1 
HETATM 2 C C5' 8LK . . . V 2 73.528 -17.018 -29.37 1 69 ? C5' 8LK 301 C 1 
HETATM 3 C C4' 8LK . . . V 2 72.096 -16.987 -28.75 1 71.16 ? C4' 8LK 301 C 1 
HETATM 4 O O4' 8LK . . . V 2 71.704 -18.262 -28.212 1 69.65 ? O4' 8LK 301 C 1 
HETATM 5 C C3' 8LK . . . V 2 72.031 -15.974 -27.575 1 70.63 ? C3' 8LK 301 C 1 
HETATM 6 O O3' 8LK . . . V 2 71.043 -15.015 -27.889 1 73.75 ? O3' 8LK 301 C 1 
HETATM 7 C C2' 8LK . . . V 2 71.56 -16.827 -26.337 1 64.96 ? C2' 8LK 301 C 1 
HETATM 8 C C1' 8LK . . . V 2 71.087 -18.131 -26.934 1 62.34 ? C1' 8LK 301 C 1 
HETATM 9 N N1 8LK . . . V 2 71.484 -19.326 -26.068 1 57.12 ? N1 8LK 301 C 1 
HETATM 10 C C2 8LK . . . V 2 70.543 -19.84 -25.049 1 58.86 ? C2 8LK 301 C 1 
HETATM 11 O O2 8LK . . . V 2 69.45 -19.269 -24.901 1 65.9 ? O2 8LK 301 C 1 
HETATM 12 N N3 8LK . . . V 2 70.912 -20.987 -24.28 1 59.9 ? N3 8LK 301 C 1 
HETATM 13 C C4 8LK . . . V 2 72.197 -21.487 -24.579 1 57.98 ? C4 8LK 301 C 1 
HETATM 14 C C5 8LK . . . V 2 73.105 -20.966 -25.553 1 53.15 ? C5 8LK 301 C 1 
HETATM 15 C C6 8LK . . . V 2 72.731 -19.898 -26.303 1 57.67 ? C6 8LK 301 C 1 
HETATM 16 C C14 8LK . . . V 2 74.291 -21.724 -25.569 1 55.46 ? C14 8LK 301 C 1 
HETATM 17 C C15 8LK . . . V 2 74.167 -22.671 -24.62 1 49.09 ? C15 8LK 301 C 1 
HETATM 18 C C16 8LK . . . V 2 75.141 -23.736 -24.271 1 43.55 ? C16 8LK 301 C 1 
HETATM 19 N N17 8LK . . . V 2 72.864 -22.556 -23.979 1 53.73 ? N17 8LK 301 C 1 
#
_model_server_stats.io_time_ms              15 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    15 
_model_server_stats.query_time_ms           442 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           19 
#