data_2YVK
#
_model_server_result.job_id            T7Mob0Jnasksxt_YkxxnmQ 
_model_server_result.datetime_utc      '2024-12-21 16:12:38' 
_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          2yvk 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":504}' 
#
_entry.id    2YVK 
#
_exptl.entry_id    2YVK 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              260.202 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            5-S-METHYL-1-O-PHOSPHONO-5-THIO-D-RIBULOSE 
_entity.pdbx_number_of_molecules    4 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          92.34 
_cell.angle_gamma         90 
_cell.entry_id            2YVK 
_cell.length_a            79.987 
_cell.length_b            84.444 
_cell.length_c            95.299 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2YVK 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
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 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,E,F,I,J 1 1 
C,D,G,H,K,L 2 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 E N N 
? 2 F N N 
? 2 G N N 
? 2 H N N 
#
_chem_comp.formula           'C6 H13 O7 P S' 
_chem_comp.formula_weight    260.202 
_chem_comp.id                MRU 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              5-S-METHYL-1-O-PHOSPHONO-5-THIO-D-RIBULOSE 
_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
O3P P1 MRU doub 237 n n 
P1 O1P MRU sing 238 n n 
P1 O2P MRU sing 239 n n 
P1 O1 MRU sing 240 n n 
O1P HO1P MRU sing 241 n n 
O2P HO2P MRU sing 242 n n 
O1 C1 MRU sing 243 n n 
C1 C2 MRU sing 244 n n 
C1 H11 MRU sing 245 n n 
C1 H12 MRU sing 246 n n 
C2 C3 MRU sing 247 n n 
C2 O2 MRU doub 248 n n 
C3 O3 MRU sing 249 n n 
C3 C4 MRU sing 250 n n 
C3 H3 MRU sing 251 n n 
O3 HO3 MRU sing 252 n n 
C4 O4 MRU sing 253 n n 
C4 C5 MRU sing 254 n n 
C4 H4 MRU sing 255 n n 
O4 HO4 MRU sing 256 n n 
C5 S1 MRU sing 257 n n 
C5 H51 MRU sing 258 n n 
C5 H52 MRU sing 259 n n 
S1 C6 MRU sing 260 n n 
C6 H61 MRU sing 261 n n 
C6 H62 MRU sing 262 n n 
C6 H63 MRU sing 263 n n 
#
_atom_sites.entry_id                     2YVK 
_atom_sites.fract_transf_matrix[1][1]    0.012502 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000511 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.011842 
_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]    0.010502 
_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
E 2 MRU A 1 501 501 MRU MRU . 
F 2 MRU B 1 502 502 MRU MRU . 
G 2 MRU C 1 503 503 MRU MRU . 
H 2 MRU D 1 504 504 MRU MRU . 
I 3 HOH A 1 502 502 HOH HOH . 
I 3 HOH A 2 503 503 HOH HOH . 
I 3 HOH A 3 504 504 HOH HOH . 
I 3 HOH A 4 505 505 HOH HOH . 
I 3 HOH A 5 506 506 HOH HOH . 
I 3 HOH A 6 507 507 HOH HOH . 
I 3 HOH A 7 508 508 HOH HOH . 
I 3 HOH A 8 509 509 HOH HOH . 
I 3 HOH A 9 510 510 HOH HOH . 
I 3 HOH A 10 511 511 HOH HOH . 
I 3 HOH A 11 512 512 HOH HOH . 
I 3 HOH A 12 513 513 HOH HOH . 
I 3 HOH A 13 514 514 HOH HOH . 
I 3 HOH A 14 515 515 HOH HOH . 
I 3 HOH A 15 516 516 HOH HOH . 
I 3 HOH A 16 517 517 HOH HOH . 
I 3 HOH A 17 518 518 HOH HOH . 
I 3 HOH A 18 519 519 HOH HOH . 
I 3 HOH A 19 520 520 HOH HOH . 
I 3 HOH A 20 521 521 HOH HOH . 
I 3 HOH A 21 522 522 HOH HOH . 
I 3 HOH A 22 523 523 HOH HOH . 
I 3 HOH A 23 524 524 HOH HOH . 
I 3 HOH A 24 525 525 HOH HOH . 
I 3 HOH A 25 526 526 HOH HOH . 
I 3 HOH A 26 527 527 HOH HOH . 
I 3 HOH A 27 528 528 HOH HOH . 
I 3 HOH A 28 529 529 HOH HOH . 
I 3 HOH A 29 530 530 HOH HOH . 
I 3 HOH A 30 531 531 HOH HOH . 
I 3 HOH A 31 532 532 HOH HOH . 
I 3 HOH A 32 533 533 HOH HOH . 
I 3 HOH A 33 534 534 HOH HOH . 
I 3 HOH A 34 535 535 HOH HOH . 
I 3 HOH A 35 536 536 HOH HOH . 
I 3 HOH A 36 537 537 HOH HOH . 
I 3 HOH A 37 538 538 HOH HOH . 
I 3 HOH A 38 539 539 HOH HOH . 
I 3 HOH A 39 540 540 HOH HOH . 
I 3 HOH A 40 541 541 HOH HOH . 
I 3 HOH A 41 542 542 HOH HOH . 
I 3 HOH A 42 543 543 HOH HOH . 
I 3 HOH A 43 544 544 HOH HOH . 
I 3 HOH A 44 545 545 HOH HOH . 
I 3 HOH A 45 546 546 HOH HOH . 
I 3 HOH A 46 547 547 HOH HOH . 
I 3 HOH A 47 548 548 HOH HOH . 
I 3 HOH A 48 549 549 HOH HOH . 
I 3 HOH A 49 550 550 HOH HOH . 
I 3 HOH A 50 551 551 HOH HOH . 
I 3 HOH A 51 552 552 HOH HOH . 
I 3 HOH A 52 553 553 HOH HOH . 
I 3 HOH A 53 554 554 HOH HOH . 
I 3 HOH A 54 555 555 HOH HOH . 
I 3 HOH A 55 556 556 HOH HOH . 
I 3 HOH A 56 557 557 HOH HOH . 
I 3 HOH A 57 558 558 HOH HOH . 
I 3 HOH A 58 559 559 HOH HOH . 
I 3 HOH A 59 560 560 HOH HOH . 
I 3 HOH A 60 561 561 HOH HOH . 
I 3 HOH A 61 562 562 HOH HOH . 
J 3 HOH B 1 503 503 HOH HOH . 
J 3 HOH B 2 504 504 HOH HOH . 
J 3 HOH B 3 505 505 HOH HOH . 
J 3 HOH B 4 506 506 HOH HOH . 
J 3 HOH B 5 507 507 HOH HOH . 
J 3 HOH B 6 508 508 HOH HOH . 
J 3 HOH B 7 509 509 HOH HOH . 
J 3 HOH B 8 510 510 HOH HOH . 
J 3 HOH B 9 511 511 HOH HOH . 
J 3 HOH B 10 512 512 HOH HOH . 
J 3 HOH B 11 513 513 HOH HOH . 
J 3 HOH B 12 514 514 HOH HOH . 
J 3 HOH B 13 515 515 HOH HOH . 
J 3 HOH B 14 516 516 HOH HOH . 
J 3 HOH B 15 517 517 HOH HOH . 
J 3 HOH B 16 518 518 HOH HOH . 
J 3 HOH B 17 519 519 HOH HOH . 
J 3 HOH B 18 520 520 HOH HOH . 
J 3 HOH B 19 521 521 HOH HOH . 
J 3 HOH B 20 522 522 HOH HOH . 
J 3 HOH B 21 523 523 HOH HOH . 
J 3 HOH B 22 524 524 HOH HOH . 
J 3 HOH B 23 525 525 HOH HOH . 
J 3 HOH B 24 526 526 HOH HOH . 
J 3 HOH B 25 527 527 HOH HOH . 
J 3 HOH B 26 528 528 HOH HOH . 
J 3 HOH B 27 529 529 HOH HOH . 
J 3 HOH B 28 530 530 HOH HOH . 
J 3 HOH B 29 531 531 HOH HOH . 
J 3 HOH B 30 532 532 HOH HOH . 
J 3 HOH B 31 533 533 HOH HOH . 
J 3 HOH B 32 534 534 HOH HOH . 
J 3 HOH B 33 535 535 HOH HOH . 
J 3 HOH B 34 536 536 HOH HOH . 
J 3 HOH B 35 537 537 HOH HOH . 
J 3 HOH B 36 538 538 HOH HOH . 
J 3 HOH B 37 539 539 HOH HOH . 
J 3 HOH B 38 540 540 HOH HOH . 
J 3 HOH B 39 541 541 HOH HOH . 
J 3 HOH B 40 542 542 HOH HOH . 
J 3 HOH B 41 543 543 HOH HOH . 
J 3 HOH B 42 544 544 HOH HOH . 
J 3 HOH B 43 545 545 HOH HOH . 
J 3 HOH B 44 546 546 HOH HOH . 
J 3 HOH B 45 547 547 HOH HOH . 
J 3 HOH B 46 548 548 HOH HOH . 
J 3 HOH B 47 549 549 HOH HOH . 
J 3 HOH B 48 550 550 HOH HOH . 
J 3 HOH B 49 551 551 HOH HOH . 
J 3 HOH B 50 552 552 HOH HOH . 
J 3 HOH B 51 553 553 HOH HOH . 
J 3 HOH B 52 554 554 HOH HOH . 
J 3 HOH B 53 555 555 HOH HOH . 
J 3 HOH B 54 556 556 HOH HOH . 
J 3 HOH B 55 557 557 HOH HOH . 
J 3 HOH B 56 558 558 HOH HOH . 
K 3 HOH C 1 504 504 HOH HOH . 
K 3 HOH C 2 505 505 HOH HOH . 
K 3 HOH C 3 506 506 HOH HOH . 
K 3 HOH C 4 507 507 HOH HOH . 
K 3 HOH C 5 508 508 HOH HOH . 
K 3 HOH C 6 509 509 HOH HOH . 
K 3 HOH C 7 510 510 HOH HOH . 
K 3 HOH C 8 511 511 HOH HOH . 
K 3 HOH C 9 512 512 HOH HOH . 
K 3 HOH C 10 513 513 HOH HOH . 
K 3 HOH C 11 514 514 HOH HOH . 
K 3 HOH C 12 515 515 HOH HOH . 
K 3 HOH C 13 516 516 HOH HOH . 
K 3 HOH C 14 517 517 HOH HOH . 
K 3 HOH C 15 518 518 HOH HOH . 
K 3 HOH C 16 519 519 HOH HOH . 
K 3 HOH C 17 520 520 HOH HOH . 
K 3 HOH C 18 521 521 HOH HOH . 
K 3 HOH C 19 522 522 HOH HOH . 
K 3 HOH C 20 523 523 HOH HOH . 
K 3 HOH C 21 524 524 HOH HOH . 
K 3 HOH C 22 525 525 HOH HOH . 
K 3 HOH C 23 526 526 HOH HOH . 
K 3 HOH C 24 527 527 HOH HOH . 
K 3 HOH C 25 528 528 HOH HOH . 
K 3 HOH C 26 529 529 HOH HOH . 
K 3 HOH C 27 530 530 HOH HOH . 
K 3 HOH C 28 531 531 HOH HOH . 
K 3 HOH C 29 532 532 HOH HOH . 
K 3 HOH C 30 533 533 HOH HOH . 
K 3 HOH C 31 534 534 HOH HOH . 
K 3 HOH C 32 535 535 HOH HOH . 
K 3 HOH C 33 536 536 HOH HOH . 
K 3 HOH C 34 537 537 HOH HOH . 
K 3 HOH C 35 538 538 HOH HOH . 
K 3 HOH C 36 539 539 HOH HOH . 
K 3 HOH C 37 540 540 HOH HOH . 
K 3 HOH C 38 541 541 HOH HOH . 
K 3 HOH C 39 542 542 HOH HOH . 
K 3 HOH C 40 543 543 HOH HOH . 
K 3 HOH C 41 544 544 HOH HOH . 
K 3 HOH C 42 545 545 HOH HOH . 
K 3 HOH C 43 546 546 HOH HOH . 
K 3 HOH C 44 547 547 HOH HOH . 
K 3 HOH C 45 548 548 HOH HOH . 
K 3 HOH C 46 549 549 HOH HOH . 
K 3 HOH C 47 550 550 HOH HOH . 
K 3 HOH C 48 551 551 HOH HOH . 
K 3 HOH C 49 552 552 HOH HOH . 
K 3 HOH C 50 553 553 HOH HOH . 
K 3 HOH C 51 554 554 HOH HOH . 
K 3 HOH C 52 555 555 HOH HOH . 
K 3 HOH C 53 556 556 HOH HOH . 
K 3 HOH C 54 557 557 HOH HOH . 
K 3 HOH C 55 558 558 HOH HOH . 
K 3 HOH C 56 559 559 HOH HOH . 
K 3 HOH C 57 560 560 HOH HOH . 
K 3 HOH C 58 561 561 HOH HOH . 
K 3 HOH C 59 562 562 HOH HOH . 
K 3 HOH C 60 563 563 HOH HOH . 
K 3 HOH C 61 564 564 HOH HOH . 
K 3 HOH C 62 565 565 HOH HOH . 
K 3 HOH C 63 566 566 HOH HOH . 
K 3 HOH C 64 567 567 HOH HOH . 
K 3 HOH C 65 568 568 HOH HOH . 
K 3 HOH C 66 569 569 HOH HOH . 
K 3 HOH C 67 570 570 HOH HOH . 
K 3 HOH C 68 571 571 HOH HOH . 
L 3 HOH D 1 505 505 HOH HOH . 
L 3 HOH D 2 506 506 HOH HOH . 
L 3 HOH D 3 507 507 HOH HOH . 
L 3 HOH D 4 508 508 HOH HOH . 
L 3 HOH D 5 509 509 HOH HOH . 
L 3 HOH D 6 510 510 HOH HOH . 
L 3 HOH D 7 511 511 HOH HOH . 
L 3 HOH D 8 512 512 HOH HOH . 
L 3 HOH D 9 513 513 HOH HOH . 
L 3 HOH D 10 514 514 HOH HOH . 
L 3 HOH D 11 515 515 HOH HOH . 
L 3 HOH D 12 516 516 HOH HOH . 
L 3 HOH D 13 517 517 HOH HOH . 
L 3 HOH D 14 518 518 HOH HOH . 
L 3 HOH D 15 519 519 HOH HOH . 
L 3 HOH D 16 520 520 HOH HOH . 
L 3 HOH D 17 521 521 HOH HOH . 
L 3 HOH D 18 522 522 HOH HOH . 
L 3 HOH D 19 523 523 HOH HOH . 
L 3 HOH D 20 524 524 HOH HOH . 
L 3 HOH D 21 525 525 HOH HOH . 
L 3 HOH D 22 526 526 HOH HOH . 
L 3 HOH D 23 527 527 HOH HOH . 
L 3 HOH D 24 528 528 HOH HOH . 
L 3 HOH D 25 529 529 HOH HOH . 
L 3 HOH D 26 530 530 HOH HOH . 
L 3 HOH D 27 531 531 HOH HOH . 
L 3 HOH D 28 532 532 HOH HOH . 
L 3 HOH D 29 533 533 HOH HOH . 
L 3 HOH D 30 534 534 HOH HOH . 
L 3 HOH D 31 535 535 HOH HOH . 
L 3 HOH D 32 536 536 HOH HOH . 
L 3 HOH D 33 537 537 HOH HOH . 
L 3 HOH D 34 538 538 HOH HOH . 
L 3 HOH D 35 539 539 HOH HOH . 
L 3 HOH D 36 540 540 HOH HOH . 
L 3 HOH D 37 541 541 HOH HOH . 
L 3 HOH D 38 542 542 HOH HOH . 
L 3 HOH D 39 543 543 HOH HOH . 
L 3 HOH D 40 544 544 HOH HOH . 
L 3 HOH D 41 545 545 HOH HOH . 
L 3 HOH D 42 546 546 HOH HOH . 
L 3 HOH D 43 547 547 HOH HOH . 
L 3 HOH D 44 548 548 HOH HOH . 
L 3 HOH D 45 549 549 HOH HOH . 
L 3 HOH D 46 550 550 HOH HOH . 
L 3 HOH D 47 551 551 HOH HOH . 
L 3 HOH D 48 552 552 HOH HOH . 
L 3 HOH D 49 553 553 HOH HOH . 
L 3 HOH D 50 554 554 HOH HOH . 
L 3 HOH D 51 555 555 HOH HOH . 
L 3 HOH D 52 556 556 HOH HOH . 
L 3 HOH D 53 557 557 HOH HOH . 
L 3 HOH D 54 558 558 HOH HOH . 
L 3 HOH D 55 559 559 HOH HOH . 
L 3 HOH D 56 560 560 HOH HOH . 
L 3 HOH D 57 561 561 HOH HOH . 
L 3 HOH D 58 562 562 HOH HOH . 
L 3 HOH D 59 563 563 HOH HOH . 
L 3 HOH D 60 564 564 HOH HOH . 
L 3 HOH D 61 565 565 HOH HOH . 
L 3 HOH D 62 566 566 HOH HOH . 
L 3 HOH D 63 567 567 HOH HOH . 
L 3 HOH D 64 568 568 HOH HOH . 
L 3 HOH D 65 569 569 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 O3P MRU . . . H 2 28.886 4.745 34.476 1 41 ? O3P MRU 504 D 1 
HETATM 2 P P1 MRU . . . H 2 27.588 5.297 35.015 1 43.21 ? P1 MRU 504 D 1 
HETATM 3 O O1P MRU . . . H 2 27.682 6.71 35.54 1 40.63 ? O1P MRU 504 D 1 
HETATM 4 O O2P MRU . . . H 2 26.387 5.036 34.138 1 41.96 ? O2P MRU 504 D 1 
HETATM 5 O O1 MRU . . . H 2 27.307 4.412 36.331 1 45.32 ? O1 MRU 504 D 1 
HETATM 6 C C1 MRU . . . H 2 28.368 4.091 37.228 1 49.34 ? C1 MRU 504 D 1 
HETATM 7 C C2 MRU . . . H 2 27.846 3.197 38.326 1 51.02 ? C2 MRU 504 D 1 
HETATM 8 O O2 MRU . . . H 2 26.791 3.46 38.881 1 52.08 ? O2 MRU 504 D 1 
HETATM 9 C C3 MRU . . . H 2 28.629 1.984 38.732 1 51.43 ? C3 MRU 504 D 1 
HETATM 10 O O3 MRU . . . H 2 27.805 1.131 39.535 1 49.44 ? O3 MRU 504 D 1 
HETATM 11 C C4 MRU . . . H 2 29.85 2.414 39.536 1 51.76 ? C4 MRU 504 D 1 
HETATM 12 O O4 MRU . . . H 2 30.384 3.622 38.984 1 50.94 ? O4 MRU 504 D 1 
HETATM 13 C C5 MRU . . . H 2 30.922 1.331 39.521 1 52.87 ? C5 MRU 504 D 1 
HETATM 14 S S1 MRU . . . H 2 30.9 0.502 37.967 1 54.31 ? S1 MRU 504 D 1 
HETATM 15 C C6 MRU . . . H 2 32.545 0.074 37.505 1 54.33 ? C6 MRU 504 D 1 
#
_model_server_stats.io_time_ms              16 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    24 
_model_server_stats.query_time_ms           332 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           15 
#