data_6EMA
#
_model_server_result.job_id            Ep4heQ5xfiMfnFqD5rgEFg 
_model_server_result.datetime_utc      '2024-11-24 05:46:31' 
_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          6ema 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":101}' 
#
_entry.id    6EMA 
#
_exptl.entry_id    6EMA 
_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-ribopyranose 
_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            6EMA 
_cell.length_a            68.86 
_cell.length_b            73.433 
_cell.length_c            76.94 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6EMA 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_pdbx_struct_assembly.details               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 
#
_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 
#
_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
covale ? covale1 A C PHE 141 A PHE 138 1_555 A N SEP 142 A SEP 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? 
covale ? covale2 A C SEP 142 A SEP 139 1_555 A N GLU 143 A GLU 140 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? 
covale ? covale3 A C TRP 199 A TRP 196 1_555 A N TPO 200 A TPO 197 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? 
covale ? covale4 A C TPO 200 A TPO 197 1_555 A N LEU 201 A LEU 198 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? 
covale ? covale5 A C VAL 340 A VAL 337 1_555 A N SEP 341 A SEP 338 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? 
covale ? covale6 A C SEP 341 A SEP 338 1_555 A N ILE 342 A ILE 339 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? 
#
_chem_comp.formula           'C5 H10 O5' 
_chem_comp.formula_weight    150.13 
_chem_comp.id                RIP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              beta-D-ribopyranose 
_chem_comp.type              'd-saccharide, beta linking' 
_chem_comp.pdbx_synonyms     'beta-D-ribose;D-ribose;ribose;RIBOSE(PYRANOSE FORM)' 
#
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 RIP sing 326 n n 
C1 O1 RIP sing 327 n n 
C1 O5 RIP sing 328 n n 
C1 H1 RIP sing 329 n n 
C2 C3 RIP sing 330 n n 
C2 O2 RIP sing 331 n n 
C2 H2 RIP sing 332 n n 
C3 C4 RIP sing 333 n n 
C3 O3 RIP sing 334 n n 
C3 H3 RIP sing 335 n n 
C4 C5 RIP sing 336 n n 
C4 O4 RIP sing 337 n n 
C4 H4 RIP sing 338 n n 
C5 O5 RIP sing 339 n n 
C5 H51 RIP sing 340 n n 
C5 H52 RIP sing 341 n n 
O1 HO1 RIP sing 342 n n 
O2 HO2 RIP sing 343 n n 
O3 HO3 RIP sing 344 n n 
O4 HO4 RIP sing 345 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
RIP DRibpb 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1 
RIP b-D-ribopyranose 'COMMON NAME' GMML 1 
RIP b-D-Ribp 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1 
RIP Rib 'SNFG CARBOHYDRATE SYMBOL' GMML 1 
#
_atom_sites.entry_id                     6EMA 
_atom_sites.fract_transf_matrix[1][1]    0.014522 
_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]    0.013618 
_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]    0.012997 
_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
C 3 ATP A 1 401 1 ATP ATP . 
D 4 RIP C 1 101 1 RIP RIB . 
E 5 HOH A 1 501 111 HOH HOH . 
E 5 HOH A 2 502 83 HOH HOH . 
E 5 HOH A 3 503 21 HOH HOH . 
E 5 HOH A 4 504 91 HOH HOH . 
E 5 HOH A 5 505 47 HOH HOH . 
E 5 HOH A 6 506 75 HOH HOH . 
E 5 HOH A 7 507 3 HOH HOH . 
E 5 HOH A 8 508 46 HOH HOH . 
E 5 HOH A 9 509 76 HOH HOH . 
E 5 HOH A 10 510 54 HOH HOH . 
E 5 HOH A 11 511 99 HOH HOH . 
E 5 HOH A 12 512 26 HOH HOH . 
E 5 HOH A 13 513 50 HOH HOH . 
E 5 HOH A 14 514 14 HOH HOH . 
E 5 HOH A 15 515 53 HOH HOH . 
E 5 HOH A 16 516 52 HOH HOH . 
E 5 HOH A 17 517 42 HOH HOH . 
E 5 HOH A 18 518 104 HOH HOH . 
E 5 HOH A 19 519 45 HOH HOH . 
E 5 HOH A 20 520 22 HOH HOH . 
E 5 HOH A 21 521 17 HOH HOH . 
E 5 HOH A 22 522 72 HOH HOH . 
E 5 HOH A 23 523 126 HOH HOH . 
E 5 HOH A 24 524 8 HOH HOH . 
E 5 HOH A 25 525 19 HOH HOH . 
E 5 HOH A 26 526 66 HOH HOH . 
E 5 HOH A 27 527 43 HOH HOH . 
E 5 HOH A 28 528 57 HOH HOH . 
E 5 HOH A 29 529 5 HOH HOH . 
E 5 HOH A 30 530 36 HOH HOH . 
E 5 HOH A 31 531 103 HOH HOH . 
E 5 HOH A 32 532 69 HOH HOH . 
E 5 HOH A 33 533 16 HOH HOH . 
E 5 HOH A 34 534 4 HOH HOH . 
E 5 HOH A 35 535 95 HOH HOH . 
E 5 HOH A 36 536 6 HOH HOH . 
E 5 HOH A 37 537 35 HOH HOH . 
E 5 HOH A 38 538 118 HOH HOH . 
E 5 HOH A 39 539 41 HOH HOH . 
E 5 HOH A 40 540 25 HOH HOH . 
E 5 HOH A 41 541 62 HOH HOH . 
E 5 HOH A 42 542 28 HOH HOH . 
E 5 HOH A 43 543 2 HOH HOH . 
E 5 HOH A 44 544 78 HOH HOH . 
E 5 HOH A 45 545 20 HOH HOH . 
E 5 HOH A 46 546 7 HOH HOH . 
E 5 HOH A 47 547 15 HOH HOH . 
E 5 HOH A 48 548 9 HOH HOH . 
E 5 HOH A 49 549 127 HOH HOH . 
E 5 HOH A 50 550 80 HOH HOH . 
E 5 HOH A 51 551 56 HOH HOH . 
E 5 HOH A 52 552 31 HOH HOH . 
E 5 HOH A 53 553 39 HOH HOH . 
E 5 HOH A 54 554 12 HOH HOH . 
E 5 HOH A 55 555 82 HOH HOH . 
E 5 HOH A 56 556 27 HOH HOH . 
E 5 HOH A 57 557 60 HOH HOH . 
E 5 HOH A 58 558 88 HOH HOH . 
E 5 HOH A 59 559 10 HOH HOH . 
E 5 HOH A 60 560 125 HOH HOH . 
E 5 HOH A 61 561 74 HOH HOH . 
E 5 HOH A 62 562 40 HOH HOH . 
E 5 HOH A 63 563 79 HOH HOH . 
E 5 HOH A 64 564 65 HOH HOH . 
E 5 HOH A 65 565 110 HOH HOH . 
E 5 HOH A 66 566 61 HOH HOH . 
E 5 HOH A 67 567 92 HOH HOH . 
E 5 HOH A 68 568 32 HOH HOH . 
E 5 HOH A 69 569 23 HOH HOH . 
E 5 HOH A 70 570 37 HOH HOH . 
E 5 HOH A 71 571 116 HOH HOH . 
E 5 HOH A 72 572 51 HOH HOH . 
E 5 HOH A 73 573 67 HOH HOH . 
E 5 HOH A 74 574 114 HOH HOH . 
E 5 HOH A 75 575 63 HOH HOH . 
E 5 HOH A 76 576 87 HOH HOH . 
E 5 HOH A 77 577 107 HOH HOH . 
E 5 HOH A 78 578 101 HOH HOH . 
E 5 HOH A 79 579 59 HOH HOH . 
E 5 HOH A 80 580 100 HOH HOH . 
E 5 HOH A 81 581 24 HOH HOH . 
E 5 HOH A 82 582 77 HOH HOH . 
E 5 HOH A 83 583 29 HOH HOH . 
E 5 HOH A 84 584 97 HOH HOH . 
E 5 HOH A 85 585 73 HOH HOH . 
E 5 HOH A 86 586 113 HOH HOH . 
E 5 HOH A 87 587 44 HOH HOH . 
E 5 HOH A 88 588 13 HOH HOH . 
E 5 HOH A 89 589 38 HOH HOH . 
E 5 HOH A 90 590 18 HOH HOH . 
E 5 HOH A 91 591 86 HOH HOH . 
E 5 HOH A 92 592 115 HOH HOH . 
E 5 HOH A 93 593 11 HOH HOH . 
E 5 HOH A 94 594 34 HOH HOH . 
E 5 HOH A 95 595 96 HOH HOH . 
E 5 HOH A 96 596 98 HOH HOH . 
E 5 HOH A 97 597 122 HOH HOH . 
E 5 HOH A 98 598 58 HOH HOH . 
E 5 HOH A 99 599 123 HOH HOH . 
E 5 HOH A 100 600 81 HOH HOH . 
E 5 HOH A 101 601 71 HOH HOH . 
E 5 HOH A 102 602 128 HOH HOH . 
E 5 HOH A 103 603 85 HOH HOH . 
E 5 HOH A 104 604 109 HOH HOH . 
E 5 HOH A 105 605 93 HOH HOH . 
E 5 HOH A 106 606 94 HOH HOH . 
E 5 HOH A 107 607 106 HOH HOH . 
F 5 HOH C 1 201 48 HOH HOH . 
F 5 HOH C 2 202 120 HOH HOH . 
F 5 HOH C 3 203 1 HOH HOH . 
F 5 HOH C 4 204 105 HOH HOH . 
F 5 HOH C 5 205 108 HOH HOH . 
F 5 HOH C 6 206 70 HOH HOH . 
F 5 HOH C 7 207 64 HOH HOH . 
F 5 HOH C 8 208 121 HOH HOH . 
F 5 HOH C 9 209 30 HOH HOH . 
F 5 HOH C 10 210 124 HOH HOH . 
F 5 HOH C 11 211 102 HOH HOH . 
F 5 HOH C 12 212 119 HOH HOH . 
F 5 HOH C 13 213 33 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 RIP . . . D 4 -3.017 12.887 11.665 1 80.83 ? C1 RIP 101 C 1 
HETATM 2 C C2 RIP . . . D 4 -3.034 11.449 11.22 1 71.49 ? C2 RIP 101 C 1 
HETATM 3 C C3 RIP . . . D 4 -4.11 11.301 10.155 1 67.36 ? C3 RIP 101 C 1 
HETATM 4 C C4 RIP . . . D 4 -3.833 12.237 8.987 1 72.44 ? C4 RIP 101 C 1 
HETATM 5 C C5 RIP . . . D 4 -3.69 13.662 9.493 1 80.62 ? C5 RIP 101 C 1 
HETATM 6 O O1 RIP . . . D 4 -4.291 13.038 12.182 1 67.84 ? O1 RIP 101 C 1 
HETATM 7 O O2 RIP . . . D 4 -1.748 11.077 10.739 1 71.6 ? O2 RIP 101 C 1 
HETATM 8 O O3 RIP . . . D 4 -4.185 9.953 9.708 1 75.76 ? O3 RIP 101 C 1 
HETATM 9 O O4 RIP . . . D 4 -2.635 11.848 8.315 1 80.05 ? O4 RIP 101 C 1 
HETATM 10 O O5 RIP . . . D 4 -2.737 13.752 10.563 1 92.32 ? O5 RIP 101 C 1 
HETATM 11 H H1 RIP . . . D 4 -2.305 13.045 12.475 1 97 ? H1 RIP 101 C 1 
HETATM 12 H H2 RIP . . . D 4 -3.303 10.809 12.059 1 85.78 ? H2 RIP 101 C 1 
HETATM 13 H H3 RIP . . . D 4 -5.073 11.57 10.587 1 80.83 ? H3 RIP 101 C 1 
HETATM 14 H H4 RIP . . . D 4 -4.6 12.146 8.22 1 86.93 ? H4 RIP 101 C 1 
HETATM 15 H H51 RIP . . . D 4 -3.27 14.328 8.741 1 96.75 ? H51 RIP 101 C 1 
HETATM 16 H H52 RIP . . . D 4 -4.645 14.087 9.798 1 96.75 ? H52 RIP 101 C 1 
HETATM 17 H HO1 RIP . . . D 4 -4.889 13.43 11.494 1 81.41 ? HO1 RIP 101 C 1 
HETATM 18 H HO2 RIP . . . D 4 -1.257 10.684 11.507 1 85.92 ? HO2 RIP 101 C 1 
HETATM 19 H HO3 RIP . . . D 4 -4.996 9.554 10.119 1 90.91 ? HO3 RIP 101 C 1 
HETATM 20 H HO4 RIP . . . D 4 -2.805 11.828 7.337 1 96.05 ? HO4 RIP 101 C 1 
#
_model_server_stats.io_time_ms              55 
_model_server_stats.parse_time_ms           22 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           231 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           20 
#