data_4H55
#
_model_server_result.job_id            E1xe1TkFoF7dKICRYW8U2Q 
_model_server_result.datetime_utc      '2024-11-28 10:08:20' 
_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          4h55 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":303}' 
#
_entry.id    4H55 
#
_exptl.entry_id    4H55 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              150.13 
_entity.id                          4 
_entity.src_method                  man 
_entity.type                        non-polymer 
_entity.pdbx_description            beta-D-ribofuranose 
_entity.pdbx_number_of_molecules    1 
_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            4H55 
_cell.length_a            67.24 
_cell.length_b            70.43 
_cell.length_c            97.57 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4H55 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        23 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'I 2 2 2' 
#
_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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2,3,4 
#
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' 2_665 -x+1,-y+1,z -1 0 0 0 -1 0 0 0 1 67.24 70.43 0 
3 'crystal symmetry operation' 3_655 -x+1,y,-z -1 0 0 0 1 0 0 0 -1 67.24 0 0 
4 'crystal symmetry operation' 4_565 x,-y+1,-z 1 0 0 0 -1 0 0 0 -1 0 70.43 0 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      4 
_struct_asym.id                             D 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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 OE2 GLU 8 A GLU 8 1_555 C MN MN . A MN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.101 ? 
metalc ? metalc2 A OD1 ASP 10 A ASP 10 1_555 B CA CA . A CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.418 ? 
metalc ? metalc3 A OD2 ASP 10 A ASP 10 1_555 B CA CA . A CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.536 ? 
metalc ? metalc4 A OD2 ASP 10 A ASP 10 1_555 C MN MN . A MN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? 
metalc ? metalc5 A O TYR 12 A TYR 12 1_555 B CA CA . A CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.427 ? 
metalc ? metalc6 A OD1 ASN 14 A ASN 14 1_555 B CA CA . A CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? 
metalc ? metalc7 A OD2 ASP 19 A ASP 19 1_555 B CA CA . A CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.337 ? 
metalc ? metalc8 A OD1 ASP 19 A ASP 19 1_555 C MN MN . A MN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.277 ? 
metalc ? metalc9 A NE2 HIS 24 A HIS 24 1_555 C MN MN . A MN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? 
metalc ? metalc10 B CA CA . A CA 301 1_555 F O HOH . A HOH 458 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? 
metalc ? metalc11 B CA CA . A CA 301 1_555 F O HOH . A HOH 479 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.283 ? 
metalc ? metalc12 C MN MN . A MN 302 1_555 F O HOH . A HOH 477 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.396 ? 
metalc ? metalc13 C MN MN . A MN 302 1_555 F O HOH . A HOH 480 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.392 ? 
#
_chem_comp.formula           'C5 H10 O5' 
_chem_comp.formula_weight    150.13 
_chem_comp.id                BDR 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              beta-D-ribofuranose 
_chem_comp.type              'd-saccharide, beta linking' 
_chem_comp.pdbx_synonyms     beta-D-ribose;D-ribose;ribose;BETA-D-RIBOFURANOSYL 
#
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
C4 O4 BDR sing 70 n n 
C4 C3 BDR sing 71 n n 
C4 C5 BDR sing 72 n n 
C4 H4 BDR sing 73 n n 
O4 C1 BDR sing 74 n n 
C1 O1 BDR sing 75 n n 
C1 C2 BDR sing 76 n n 
C1 H1 BDR sing 77 n n 
O1 HO1 BDR sing 78 n n 
C2 O2 BDR sing 79 n n 
C2 C3 BDR sing 80 n n 
C2 H2 BDR sing 81 n n 
O2 HO2 BDR sing 82 n n 
C3 O3 BDR sing 83 n n 
C3 H3 BDR sing 84 n n 
O3 HO3 BDR sing 85 n n 
C5 O5 BDR sing 86 n n 
C5 H51 BDR sing 87 n n 
C5 H52 BDR sing 88 n n 
O5 HO5 BDR sing 89 n n 
#
loop_
_pdbx_chem_comp_identifier.comp_id
_pdbx_chem_comp_identifier.identifier
_pdbx_chem_comp_identifier.type
_pdbx_chem_comp_identifier.program
_pdbx_chem_comp_identifier.program_version
BDR DRibfb 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1 
BDR b-D-ribofuranose 'COMMON NAME' GMML 1 
BDR b-D-Ribf 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1 
BDR Rib 'SNFG CARBOHYDRATE SYMBOL' GMML 1 
#
_atom_sites.entry_id                     4H55 
_atom_sites.fract_transf_matrix[1][1]    0.014872 
_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]    0.014198 
_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]    0.010249 
_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
B 2 CA A 1 301 240 CA CA . 
C 3 MN A 1 302 241 MN MN . 
D 4 BDR A 1 303 242 BDR BDR . 
E 5 DBB A 1 304 903 DBB DBB . 
F 6 HOH A 1 401 1 HOH HOH . 
F 6 HOH A 2 402 2 HOH HOH . 
F 6 HOH A 3 403 3 HOH HOH . 
F 6 HOH A 4 404 4 HOH HOH . 
F 6 HOH A 5 405 5 HOH HOH . 
F 6 HOH A 6 406 6 HOH HOH . 
F 6 HOH A 7 407 7 HOH HOH . 
F 6 HOH A 8 408 8 HOH HOH . 
F 6 HOH A 9 409 9 HOH HOH . 
F 6 HOH A 10 410 10 HOH HOH . 
F 6 HOH A 11 411 11 HOH HOH . 
F 6 HOH A 12 412 12 HOH HOH . 
F 6 HOH A 13 413 13 HOH HOH . 
F 6 HOH A 14 414 14 HOH HOH . 
F 6 HOH A 15 415 15 HOH HOH . 
F 6 HOH A 16 416 16 HOH HOH . 
F 6 HOH A 17 417 17 HOH HOH . 
F 6 HOH A 18 418 18 HOH HOH . 
F 6 HOH A 19 419 19 HOH HOH . 
F 6 HOH A 20 420 20 HOH HOH . 
F 6 HOH A 21 421 21 HOH HOH . 
F 6 HOH A 22 422 22 HOH HOH . 
F 6 HOH A 23 423 23 HOH HOH . 
F 6 HOH A 24 424 24 HOH HOH . 
F 6 HOH A 25 425 25 HOH HOH . 
F 6 HOH A 26 426 26 HOH HOH . 
F 6 HOH A 27 427 27 HOH HOH . 
F 6 HOH A 28 428 28 HOH HOH . 
F 6 HOH A 29 429 29 HOH HOH . 
F 6 HOH A 30 430 30 HOH HOH . 
F 6 HOH A 31 431 31 HOH HOH . 
F 6 HOH A 32 432 32 HOH HOH . 
F 6 HOH A 33 433 33 HOH HOH . 
F 6 HOH A 34 434 34 HOH HOH . 
F 6 HOH A 35 435 35 HOH HOH . 
F 6 HOH A 36 436 36 HOH HOH . 
F 6 HOH A 37 437 37 HOH HOH . 
F 6 HOH A 38 438 38 HOH HOH . 
F 6 HOH A 39 439 39 HOH HOH . 
F 6 HOH A 40 440 40 HOH HOH . 
F 6 HOH A 41 441 41 HOH HOH . 
F 6 HOH A 42 442 42 HOH HOH . 
F 6 HOH A 43 443 43 HOH HOH . 
F 6 HOH A 44 444 44 HOH HOH . 
F 6 HOH A 45 445 45 HOH HOH . 
F 6 HOH A 46 446 46 HOH HOH . 
F 6 HOH A 47 447 47 HOH HOH . 
F 6 HOH A 48 448 48 HOH HOH . 
F 6 HOH A 49 449 49 HOH HOH . 
F 6 HOH A 50 450 50 HOH HOH . 
F 6 HOH A 51 451 51 HOH HOH . 
F 6 HOH A 52 452 52 HOH HOH . 
F 6 HOH A 53 453 53 HOH HOH . 
F 6 HOH A 54 454 54 HOH HOH . 
F 6 HOH A 55 455 55 HOH HOH . 
F 6 HOH A 56 456 56 HOH HOH . 
F 6 HOH A 57 457 57 HOH HOH . 
F 6 HOH A 58 458 58 HOH HOH . 
F 6 HOH A 59 459 59 HOH HOH . 
F 6 HOH A 60 460 60 HOH HOH . 
F 6 HOH A 61 461 61 HOH HOH . 
F 6 HOH A 62 462 62 HOH HOH . 
F 6 HOH A 63 463 63 HOH HOH . 
F 6 HOH A 64 464 64 HOH HOH . 
F 6 HOH A 65 465 65 HOH HOH . 
F 6 HOH A 66 466 66 HOH HOH . 
F 6 HOH A 67 467 67 HOH HOH . 
F 6 HOH A 68 468 68 HOH HOH . 
F 6 HOH A 69 469 69 HOH HOH . 
F 6 HOH A 70 470 70 HOH HOH . 
F 6 HOH A 71 471 71 HOH HOH . 
F 6 HOH A 72 472 72 HOH HOH . 
F 6 HOH A 73 473 73 HOH HOH . 
F 6 HOH A 74 474 74 HOH HOH . 
F 6 HOH A 75 475 75 HOH HOH . 
F 6 HOH A 76 476 76 HOH HOH . 
F 6 HOH A 77 477 77 HOH HOH . 
F 6 HOH A 78 478 78 HOH HOH . 
F 6 HOH A 79 479 79 HOH HOH . 
F 6 HOH A 80 480 80 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 C4 BDR . . . D 4 10.026 12.098 23.234 1 35.87 ? C4 BDR 303 A 1 
HETATM 2 O O4 BDR . . . D 4 10.076 13.429 23.75 1 37.39 ? O4 BDR 303 A 1 
HETATM 3 C C1 BDR . . . D 4 11.449 13.719 23.852 1 35.99 ? C1 BDR 303 A 1 
HETATM 4 O O1 BDR . . . D 4 11.705 14.95 24.505 1 41.41 ? O1 BDR 303 A 1 
HETATM 5 C C2 BDR . . . D 4 11.843 12.535 24.636 1 35.57 ? C2 BDR 303 A 1 
HETATM 6 O O2 BDR . . . D 4 13.233 12.613 24.854 1 39.1 ? O2 BDR 303 A 1 
HETATM 7 C C3 BDR . . . D 4 11.321 11.47 23.681 1 35.12 ? C3 BDR 303 A 1 
HETATM 8 O O3 BDR . . . D 4 12.05 11.405 22.441 1 34.22 ? O3 BDR 303 A 1 
HETATM 9 C C5 BDR . . . D 4 8.751 11.395 23.64 1 36.54 ? C5 BDR 303 A 1 
HETATM 10 O O5 BDR . . . D 4 7.766 12.07 22.827 1 37.71 ? O5 BDR 303 A 1 
#
_model_server_stats.io_time_ms              57 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           766 
_model_server_stats.encode_time_ms          10 
_model_server_stats.element_count           10 
#