data_4YP9
#
_model_server_result.job_id            6FMrbJnFAINtJEAbjw5kGA 
_model_server_result.datetime_utc      '2024-12-26 19:05:40' 
_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          4yp9 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":403}' 
#
_entry.id    4YP9 
#
_exptl.entry_id    4YP9 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              176.94 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            1-deoxy-alpha-L-xylulofuranose-1,2-borate 
_entity.pdbx_number_of_molecules    2 
_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            4YP9 
_cell.length_a            104.732 
_cell.length_b            104.732 
_cell.length_c            69.532 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4YP9 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        78 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 43' 
#
_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,G,H,I 
_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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 E N N 
? 3 G 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
metalc ? metalc1 A OD1 ASP 197 A ASP 217 1_555 C MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.659 ? 
metalc ? metalc2 A OD2 ASP 197 A ASP 217 1_555 C MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.214 ? 
metalc ? metalc3 C MG MG . A MG 401 1_555 H O HOH . A HOH 517 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.189 ? 
metalc ? metalc4 C MG MG . A MG 401 1_555 H O HOH . A HOH 525 3_654 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? 
metalc ? metalc5 C MG MG . A MG 401 1_555 H O HOH . A HOH 529 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.208 ? 
metalc ? metalc6 C MG MG . A MG 401 1_555 H O HOH . A HOH 534 3_654 ? ? ? ? ? ? ? ? ? ? ? ? 2.163 ? 
metalc ? metalc7 D MG MG . A MG 402 1_555 H O HOH . A HOH 515 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.113 ? 
metalc ? metalc8 D MG MG . A MG 402 1_555 H O HOH . A HOH 561 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.093 ? 
metalc ? metalc9 D MG MG . A MG 402 1_555 H O HOH . A HOH 562 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? 
metalc ? metalc10 D MG MG . A MG 402 1_555 H O HOH . A HOH 583 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.128 ? 
metalc ? metalc11 B OD1 ASP 197 B ASP 217 1_555 F CA CA . B CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.03 ? 
metalc ? metalc12 B OD2 ASP 197 B ASP 217 1_555 F CA CA . B CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.238 ? 
metalc ? metalc13 F CA CA . B CA 401 1_555 I O HOH . B HOH 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.394 ? 
metalc ? metalc14 F CA CA . B CA 401 1_555 I O HOH . B HOH 528 4_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.279 ? 
metalc ? metalc15 F CA CA . B CA 401 1_555 I O HOH . B HOH 546 4_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.435 ? 
#
_chem_comp.formula           'C5 H10 B O6 -1' 
_chem_comp.formula_weight    176.94 
_chem_comp.id                A1B 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              1-deoxy-alpha-L-xylulofuranose-1,2-borate 
_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
O12 C7 A1B sing 1 n n 
C6 O5 A1B sing 2 n n 
C6 C7 A1B sing 3 n n 
O5 C4 A1B sing 4 n n 
C7 C8 A1B sing 5 n n 
C11 C4 A1B sing 6 n n 
C4 C8 A1B sing 7 n n 
C4 O3 A1B sing 8 n n 
C8 O1 A1B sing 9 n n 
O3 B A1B sing 10 n n 
O1 B A1B sing 11 n n 
B O9 A1B sing 12 n n 
B O10 A1B sing 13 n n 
C8 H1 A1B sing 14 n n 
C7 H2 A1B sing 15 n n 
O12 H3 A1B sing 16 n n 
C6 H4 A1B sing 17 n n 
C6 H5 A1B sing 18 n n 
C11 H6 A1B sing 19 n n 
C11 H7 A1B sing 20 n n 
C11 H8 A1B sing 21 n n 
O10 H9 A1B sing 22 n n 
O9 H10 A1B sing 23 n n 
#
_atom_sites.entry_id                     4YP9 
_atom_sites.fract_transf_matrix[1][1]    0.009548 
_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]    0.009548 
_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]    0.014382 
_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 2 MG A 1 401 1 MG MG . 
D 2 MG A 1 402 1 MG MG . 
E 3 A1B A 1 403 1 A1B A1B . 
F 4 CA B 1 401 1 CA CA . 
G 3 A1B B 1 402 1 A1B A1B . 
H 5 HOH A 1 501 38 HOH HOH . 
H 5 HOH A 2 502 29 HOH HOH . 
H 5 HOH A 3 503 58 HOH HOH . 
H 5 HOH A 4 504 31 HOH HOH . 
H 5 HOH A 5 505 12 HOH HOH . 
H 5 HOH A 6 506 8 HOH HOH . 
H 5 HOH A 7 507 91 HOH HOH . 
H 5 HOH A 8 508 18 HOH HOH . 
H 5 HOH A 9 509 135 HOH HOH . 
H 5 HOH A 10 510 81 HOH HOH . 
H 5 HOH A 11 511 75 HOH HOH . 
H 5 HOH A 12 512 9 HOH HOH . 
H 5 HOH A 13 513 10 HOH HOH . 
H 5 HOH A 14 514 98 HOH HOH . 
H 5 HOH A 15 515 37 HOH HOH . 
H 5 HOH A 16 516 4 HOH HOH . 
H 5 HOH A 17 517 65 HOH HOH . 
H 5 HOH A 18 518 71 HOH HOH . 
H 5 HOH A 19 519 26 HOH HOH . 
H 5 HOH A 20 520 83 HOH HOH . 
H 5 HOH A 21 521 104 HOH HOH . 
H 5 HOH A 22 522 11 HOH HOH . 
H 5 HOH A 23 523 23 HOH HOH . 
H 5 HOH A 24 524 92 HOH HOH . 
H 5 HOH A 25 525 62 HOH HOH . 
H 5 HOH A 26 526 1 HOH HOH . 
H 5 HOH A 27 527 7 HOH HOH . 
H 5 HOH A 28 528 68 HOH HOH . 
H 5 HOH A 29 529 64 HOH HOH . 
H 5 HOH A 30 530 22 HOH HOH . 
H 5 HOH A 31 531 70 HOH HOH . 
H 5 HOH A 32 532 110 HOH HOH . 
H 5 HOH A 33 533 76 HOH HOH . 
H 5 HOH A 34 534 63 HOH HOH . 
H 5 HOH A 35 535 129 HOH HOH . 
H 5 HOH A 36 536 73 HOH HOH . 
H 5 HOH A 37 537 80 HOH HOH . 
H 5 HOH A 38 538 51 HOH HOH . 
H 5 HOH A 39 539 97 HOH HOH . 
H 5 HOH A 40 540 34 HOH HOH . 
H 5 HOH A 41 541 2 HOH HOH . 
H 5 HOH A 42 542 54 HOH HOH . 
H 5 HOH A 43 543 50 HOH HOH . 
H 5 HOH A 44 544 101 HOH HOH . 
H 5 HOH A 45 545 85 HOH HOH . 
H 5 HOH A 46 546 5 HOH HOH . 
H 5 HOH A 47 547 124 HOH HOH . 
H 5 HOH A 48 548 128 HOH HOH . 
H 5 HOH A 49 549 139 HOH HOH . 
H 5 HOH A 50 550 137 HOH HOH . 
H 5 HOH A 51 551 121 HOH HOH . 
H 5 HOH A 52 552 30 HOH HOH . 
H 5 HOH A 53 553 66 HOH HOH . 
H 5 HOH A 54 554 3 HOH HOH . 
H 5 HOH A 55 555 27 HOH HOH . 
H 5 HOH A 56 556 112 HOH HOH . 
H 5 HOH A 57 557 96 HOH HOH . 
H 5 HOH A 58 558 28 HOH HOH . 
H 5 HOH A 59 559 24 HOH HOH . 
H 5 HOH A 60 560 111 HOH HOH . 
H 5 HOH A 61 561 52 HOH HOH . 
H 5 HOH A 62 562 125 HOH HOH . 
H 5 HOH A 63 563 33 HOH HOH . 
H 5 HOH A 64 564 35 HOH HOH . 
H 5 HOH A 65 565 113 HOH HOH . 
H 5 HOH A 66 566 6 HOH HOH . 
H 5 HOH A 67 567 127 HOH HOH . 
H 5 HOH A 68 568 130 HOH HOH . 
H 5 HOH A 69 569 89 HOH HOH . 
H 5 HOH A 70 570 109 HOH HOH . 
H 5 HOH A 71 571 69 HOH HOH . 
H 5 HOH A 72 572 36 HOH HOH . 
H 5 HOH A 73 573 32 HOH HOH . 
H 5 HOH A 74 574 74 HOH HOH . 
H 5 HOH A 75 575 108 HOH HOH . 
H 5 HOH A 76 576 115 HOH HOH . 
H 5 HOH A 77 577 93 HOH HOH . 
H 5 HOH A 78 578 126 HOH HOH . 
H 5 HOH A 79 579 67 HOH HOH . 
H 5 HOH A 80 580 142 HOH HOH . 
H 5 HOH A 81 581 140 HOH HOH . 
H 5 HOH A 82 582 132 HOH HOH . 
H 5 HOH A 83 583 60 HOH HOH . 
I 5 HOH B 1 501 61 HOH HOH . 
I 5 HOH B 2 502 117 HOH HOH . 
I 5 HOH B 3 503 84 HOH HOH . 
I 5 HOH B 4 504 143 HOH HOH . 
I 5 HOH B 5 505 99 HOH HOH . 
I 5 HOH B 6 506 40 HOH HOH . 
I 5 HOH B 7 507 59 HOH HOH . 
I 5 HOH B 8 508 141 HOH HOH . 
I 5 HOH B 9 509 17 HOH HOH . 
I 5 HOH B 10 510 90 HOH HOH . 
I 5 HOH B 11 511 16 HOH HOH . 
I 5 HOH B 12 512 95 HOH HOH . 
I 5 HOH B 13 513 15 HOH HOH . 
I 5 HOH B 14 514 19 HOH HOH . 
I 5 HOH B 15 515 78 HOH HOH . 
I 5 HOH B 16 516 103 HOH HOH . 
I 5 HOH B 17 517 114 HOH HOH . 
I 5 HOH B 18 518 48 HOH HOH . 
I 5 HOH B 19 519 39 HOH HOH . 
I 5 HOH B 20 520 107 HOH HOH . 
I 5 HOH B 21 521 119 HOH HOH . 
I 5 HOH B 22 522 47 HOH HOH . 
I 5 HOH B 23 523 86 HOH HOH . 
I 5 HOH B 24 524 87 HOH HOH . 
I 5 HOH B 25 525 79 HOH HOH . 
I 5 HOH B 26 526 131 HOH HOH . 
I 5 HOH B 27 527 105 HOH HOH . 
I 5 HOH B 28 528 41 HOH HOH . 
I 5 HOH B 29 529 20 HOH HOH . 
I 5 HOH B 30 530 88 HOH HOH . 
I 5 HOH B 31 531 53 HOH HOH . 
I 5 HOH B 32 532 100 HOH HOH . 
I 5 HOH B 33 533 49 HOH HOH . 
I 5 HOH B 34 534 118 HOH HOH . 
I 5 HOH B 35 535 72 HOH HOH . 
I 5 HOH B 36 536 14 HOH HOH . 
I 5 HOH B 37 537 43 HOH HOH . 
I 5 HOH B 38 538 106 HOH HOH . 
I 5 HOH B 39 539 102 HOH HOH . 
I 5 HOH B 40 540 120 HOH HOH . 
I 5 HOH B 41 541 77 HOH HOH . 
I 5 HOH B 42 542 45 HOH HOH . 
I 5 HOH B 43 543 13 HOH HOH . 
I 5 HOH B 44 544 57 HOH HOH . 
I 5 HOH B 45 545 25 HOH HOH . 
I 5 HOH B 46 546 42 HOH HOH . 
I 5 HOH B 47 547 123 HOH HOH . 
I 5 HOH B 48 548 94 HOH HOH . 
I 5 HOH B 49 549 116 HOH HOH . 
I 5 HOH B 50 550 122 HOH HOH . 
I 5 HOH B 51 551 21 HOH HOH . 
I 5 HOH B 52 552 134 HOH HOH . 
I 5 HOH B 53 553 44 HOH HOH . 
I 5 HOH B 54 554 55 HOH HOH . 
I 5 HOH B 55 555 136 HOH HOH . 
I 5 HOH B 56 556 56 HOH HOH . 
I 5 HOH B 57 557 46 HOH HOH . 
I 5 HOH B 58 558 133 HOH HOH . 
I 5 HOH B 59 559 138 HOH HOH . 
I 5 HOH B 60 560 82 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 C8 A1B . . . E 3 29.131 36.419 -11.546 1 27.07 ? C8 A1B 403 A 1 
HETATM 2 O O1 A1B . . . E 3 29.682 37.419 -10.685 1 27.57 ? O1 A1B 403 A 1 
HETATM 3 C C7 A1B . . . E 3 30.179 35.424 -11.857 1 31.76 ? C7 A1B 403 A 1 
HETATM 4 O O12 A1B . . . E 3 29.614 34.134 -12.112 1 32.2 ? O12 A1B 403 A 1 
HETATM 5 C C6 A1B . . . E 3 30.853 35.938 -13.086 1 28.97 ? C6 A1B 403 A 1 
HETATM 6 O O5 A1B . . . E 3 29.85 36.835 -13.773 1 27.24 ? O5 A1B 403 A 1 
HETATM 7 C C4 A1B . . . E 3 28.748 37.061 -12.791 1 25.07 ? C4 A1B 403 A 1 
HETATM 8 C C11 A1B . . . E 3 27.457 36.447 -13.29 1 24.07 ? C11 A1B 403 A 1 
HETATM 9 O O3 A1B . . . E 3 28.613 38.414 -12.555 1 23.4 ? O3 A1B 403 A 1 
HETATM 10 B B A1B . . . E 3 29.172 38.686 -11.206 1 24.58 ? B A1B 403 A 1 
HETATM 11 O O10 A1B . . . E 3 28.128 39.096 -10.347 1 24.03 ? O10 A1B 403 A 1 
HETATM 12 O O9 A1B . . . E 3 30.202 39.676 -11.225 1 19.92 ? O9 A1B 403 A 1 
#
_model_server_stats.io_time_ms              63 
_model_server_stats.parse_time_ms           126 
_model_server_stats.create_model_time_ms    78 
_model_server_stats.query_time_ms           319 
_model_server_stats.encode_time_ms          22 
_model_server_stats.element_count           12 
#