data_1JVI
#
_model_server_result.job_id            7-2otlw2xWLEnoko9AO3PQ 
_model_server_result.datetime_utc      '2024-10-11 01:29:52' 
_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          1jvi 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":401}' 
#
_entry.id    1JVI 
#
_exptl.entry_id    1JVI 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              267.299 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '(2S)-2-amino-4-[[(2S,3S,4R,5R)-3,4,5-trihydroxyoxolan-2-yl]methylsulfanyl]butanoic acid' 
_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         120 
_cell.entry_id            1JVI 
_cell.length_a            62.095 
_cell.length_b            62.095 
_cell.length_c            150.051 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1JVI 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        179 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 65 2 2' 
#
_pdbx_struct_assembly.method_details        PISA,PQS 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_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 
#
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' 12_564 x,x-y+1,-z-1/6 0.5 0.866025 0 0.866025 -0.5 0 0 0 -1 -31.0475 53.775847 -25.0085 
#
_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 SG CYS 41 A CYS 41 1_555 E SD HCS . A HCS 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? 
covale ? covale2 A C GLY 83 A GLY 83 1_555 A N OCS 84 A OCS 84 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? 
covale ? covale3 A C OCS 84 A OCS 84 1_555 A N GLN 85 A GLN 85 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? 
metalc ? metalc1 A NE2 HIS 54 A HIS 54 1_555 B ZN ZN . A ZN 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.236 ? 
metalc ? metalc2 A NE2 HIS 58 A HIS 58 1_555 B ZN ZN . A ZN 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.397 ? 
metalc ? metalc3 A SG CYS 126 A CYS 126 1_555 B ZN ZN . A ZN 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.422 ? 
#
_chem_comp.formula           'C9 H17 N O6 S' 
_chem_comp.formula_weight    267.299 
_chem_comp.id                RHC 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '(2S)-2-amino-4-[[(2S,3S,4R,5R)-3,4,5-trihydroxyoxolan-2-yl]methylsulfanyl]butanoic acid' 
_chem_comp.type              'd-saccharide, beta linking' 
_chem_comp.pdbx_synonyms     5-(3-AMINO-4,4-DIHYROXY-BUTYLSULFANYLMETHYL)-TETRAHYDRO-FURAN-2,3,4-TRIOL 
#
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 O1 RHC sing 309 n n 
C1 C2 RHC sing 310 n n 
C1 O4 RHC sing 311 n n 
C1 H1 RHC sing 312 n n 
O1 HO1 RHC sing 313 n n 
C2 O2 RHC sing 314 n n 
C2 C3 RHC sing 315 n n 
C2 H2 RHC sing 316 n n 
O2 HO2 RHC sing 317 n n 
C3 O3 RHC sing 318 n n 
C3 C4 RHC sing 319 n n 
C3 H3 RHC sing 320 n n 
O3 HO3 RHC sing 321 n n 
C4 O4 RHC sing 322 n n 
C4 C5 RHC sing 323 n n 
C4 H4 RHC sing 324 n n 
C5 SD RHC sing 325 n n 
C5 H51 RHC sing 326 n n 
C5 H52 RHC sing 327 n n 
N CA RHC sing 328 n n 
N HN1 RHC sing 329 n n 
N HN2 RHC sing 330 n n 
CA CB RHC sing 331 n n 
CA C RHC sing 332 n n 
CA HCA1 RHC sing 333 n n 
CB CG RHC sing 334 n n 
CB HCB1 RHC sing 335 n n 
CB HCB2 RHC sing 336 n n 
CG SD RHC sing 337 n n 
CG HCG1 RHC sing 338 n n 
CG HCG2 RHC sing 339 n n 
C O RHC doub 340 n n 
C OXT RHC sing 341 n n 
OXT HOX1 RHC sing 342 n n 
#
_atom_sites.entry_id                     1JVI 
_atom_sites.fract_transf_matrix[1][1]    0.016104 
_atom_sites.fract_transf_matrix[1][2]    0.009298 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.018596 
_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]    0.006664 
_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 ZN A 1 300 300 ZN ZN . 
C 3 SO4 A 1 501 501 SO4 SO4 . 
D 4 RHC A 1 401 401 RHC RHC . 
E 5 HCS A 1 402 402 HCS HCS . 
F 6 HOH A 1 502 1 HOH HOH . 
F 6 HOH A 2 503 2 HOH HOH . 
F 6 HOH A 3 504 3 HOH HOH . 
F 6 HOH A 4 505 4 HOH HOH . 
F 6 HOH A 5 506 5 HOH HOH . 
F 6 HOH A 6 507 6 HOH HOH . 
F 6 HOH A 7 508 7 HOH HOH . 
F 6 HOH A 8 509 8 HOH HOH . 
F 6 HOH A 9 510 9 HOH HOH . 
F 6 HOH A 10 511 10 HOH HOH . 
F 6 HOH A 11 512 11 HOH HOH . 
F 6 HOH A 12 513 12 HOH HOH . 
F 6 HOH A 13 514 13 HOH HOH . 
F 6 HOH A 14 515 14 HOH HOH . 
F 6 HOH A 15 516 15 HOH HOH . 
F 6 HOH A 16 517 16 HOH HOH . 
F 6 HOH A 17 518 17 HOH HOH . 
F 6 HOH A 18 519 18 HOH HOH . 
F 6 HOH A 19 520 19 HOH HOH . 
F 6 HOH A 20 521 20 HOH HOH . 
F 6 HOH A 21 522 21 HOH HOH . 
F 6 HOH A 22 523 22 HOH HOH . 
F 6 HOH A 23 524 23 HOH HOH . 
F 6 HOH A 24 525 24 HOH HOH . 
F 6 HOH A 25 526 25 HOH HOH . 
F 6 HOH A 26 527 26 HOH HOH . 
F 6 HOH A 27 528 27 HOH HOH . 
F 6 HOH A 28 529 28 HOH HOH . 
F 6 HOH A 29 530 29 HOH HOH . 
F 6 HOH A 30 531 30 HOH HOH . 
F 6 HOH A 31 532 31 HOH HOH . 
F 6 HOH A 32 533 32 HOH HOH . 
F 6 HOH A 33 534 33 HOH HOH . 
F 6 HOH A 34 535 34 HOH HOH . 
F 6 HOH A 35 536 35 HOH HOH . 
F 6 HOH A 36 537 36 HOH HOH . 
F 6 HOH A 37 538 37 HOH HOH . 
F 6 HOH A 38 539 38 HOH HOH . 
F 6 HOH A 39 540 39 HOH HOH . 
F 6 HOH A 40 541 40 HOH HOH . 
F 6 HOH A 41 542 41 HOH HOH . 
F 6 HOH A 42 543 42 HOH HOH . 
F 6 HOH A 43 544 43 HOH HOH . 
F 6 HOH A 44 545 44 HOH HOH . 
F 6 HOH A 45 546 45 HOH HOH . 
F 6 HOH A 46 547 46 HOH HOH . 
F 6 HOH A 47 548 47 HOH HOH . 
F 6 HOH A 48 549 48 HOH HOH . 
F 6 HOH A 49 550 49 HOH HOH . 
F 6 HOH A 50 551 50 HOH HOH . 
F 6 HOH A 51 552 51 HOH HOH . 
F 6 HOH A 52 553 52 HOH HOH . 
F 6 HOH A 53 554 53 HOH HOH . 
F 6 HOH A 54 555 54 HOH HOH . 
F 6 HOH A 55 556 55 HOH HOH . 
F 6 HOH A 56 557 56 HOH HOH . 
F 6 HOH A 57 558 57 HOH HOH . 
F 6 HOH A 58 559 58 HOH HOH . 
F 6 HOH A 59 560 59 HOH HOH . 
F 6 HOH A 60 561 60 HOH HOH . 
F 6 HOH A 61 562 61 HOH HOH . 
F 6 HOH A 62 563 62 HOH HOH . 
F 6 HOH A 63 564 63 HOH HOH . 
F 6 HOH A 64 565 64 HOH HOH . 
F 6 HOH A 65 566 65 HOH HOH . 
F 6 HOH A 66 567 66 HOH HOH . 
F 6 HOH A 67 568 67 HOH HOH . 
F 6 HOH A 68 569 68 HOH HOH . 
F 6 HOH A 69 570 69 HOH HOH . 
F 6 HOH A 70 571 70 HOH HOH . 
F 6 HOH A 71 572 71 HOH HOH . 
F 6 HOH A 72 573 72 HOH HOH . 
F 6 HOH A 73 574 73 HOH HOH . 
F 6 HOH A 74 575 74 HOH HOH . 
F 6 HOH A 75 576 75 HOH HOH . 
F 6 HOH A 76 577 76 HOH HOH . 
F 6 HOH A 77 578 77 HOH HOH . 
F 6 HOH A 78 579 78 HOH HOH . 
F 6 HOH A 79 580 79 HOH HOH . 
F 6 HOH A 80 581 80 HOH HOH . 
F 6 HOH A 81 582 81 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 RHC . . . D 4 -25.91 31.515 -19.313 1 67.51 ? C1 RHC 401 A 1 
HETATM 2 O O1 RHC . . . D 4 -25.643 32.33 -20.403 1 52.77 ? O1 RHC 401 A 1 
HETATM 3 C C2 RHC . . . D 4 -25.224 30.171 -19.485 1 64.42 ? C2 RHC 401 A 1 
HETATM 4 O O2 RHC . . . D 4 -26.124 29.267 -20.077 1 52.94 ? O2 RHC 401 A 1 
HETATM 5 C C3 RHC . . . D 4 -24.852 29.762 -18.058 1 72.2 ? C3 RHC 401 A 1 
HETATM 6 O O3 RHC . . . D 4 -25.848 28.949 -17.428 1 37.64 ? O3 RHC 401 A 1 
HETATM 7 C C4 RHC . . . D 4 -24.748 31.085 -17.315 1 71.02 ? C4 RHC 401 A 1 
HETATM 8 O O4 RHC . . . D 4 -25.35 32.11 -18.141 1 76.11 ? O4 RHC 401 A 1 
HETATM 9 C C5 RHC . . . D 4 -23.315 31.476 -17.055 1 61.73 ? C5 RHC 401 A 1 
HETATM 10 N N RHC . . . D 4 -19.334 30.515 -14.331 1 45.43 ? N RHC 401 A 1 
HETATM 11 C CA RHC . . . D 4 -19.291 31.595 -15.306 1 53.15 ? CA RHC 401 A 1 
HETATM 12 C CB RHC . . . D 4 -20.668 31.815 -15.903 1 58.92 ? CB RHC 401 A 1 
HETATM 13 C CG RHC . . . D 4 -21.749 31.989 -14.883 1 48.23 ? CG RHC 401 A 1 
HETATM 14 S SD RHC . . . D 4 -23.219 32.583 -15.716 1 51.03 ? SD RHC 401 A 1 
HETATM 15 C C RHC . . . D 4 -18.785 32.917 -14.74 1 42.94 ? C RHC 401 A 1 
HETATM 16 O O RHC . . . D 4 -18.607 33.858 -15.546 1 57.72 ? O RHC 401 A 1 
HETATM 17 O OXT RHC . . . D 4 -18.587 32.997 -13.51 1 35.62 ? OXT RHC 401 A 1 
#
_model_server_stats.io_time_ms              6 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           310 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           17 
#