data_4QNV
#
_model_server_result.job_id            BnWyQfNcOL-1Mr6Q6um5yg 
_model_server_result.datetime_utc      '2024-11-29 13:53:02' 
_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          4qnv 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":402}' 
#
_entry.id    4QNV 
#
_exptl.entry_id    4QNV 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              442.447 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '(2S)-4-[{[(2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl}(carboxylatomethyl)sulfonio] -2-ammoniobutanoate' 
_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         120 
_cell.entry_id            4QNV 
_cell.length_a            82.134 
_cell.length_b            82.134 
_cell.length_c            432.516 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4QNV 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        178 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 61 2 2' 
#
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 monomeric 1 author_and_software_defined_assembly 1 
PISA monomeric 1 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,C,D,G 1 1 
B,E,F,H 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
? 3 D N N 
? 3 F N N 
#
_chem_comp.formula           'C16 H22 N6 O7 S' 
_chem_comp.formula_weight    442.447 
_chem_comp.id                GEK 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '(2S)-4-[{[(2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl}(carboxylatomethyl)sulfonio] -2-ammoniobutanoate' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     CARBOXY-S-ADENOSYLMETHIONINE 
#
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
C O GEK sing 83 n n 
C CA GEK sing 84 n n 
C OXT GEK doub 85 n n 
N CA GEK sing 86 n n 
N HN GEK sing 87 n n 
N HNA GEK sing 88 n n 
N1 C2 GEK doub 89 n y 
N1 C6 GEK sing 90 n y 
C2 N3 GEK sing 91 n y 
C2 H2 GEK sing 92 n n 
N3 C4 GEK doub 93 n y 
C4 C5 GEK sing 94 n y 
C4 N9 GEK sing 95 n y 
C5 C6 GEK doub 96 n y 
C5 N7 GEK sing 97 n y 
C6 N6 GEK sing 98 n n 
N6 HN6 GEK sing 99 n n 
N6 HN6A GEK sing 100 n n 
N7 C8 GEK doub 101 n y 
C8 N9 GEK sing 102 n y 
C8 H8 GEK sing 103 n n 
N9 C1' GEK sing 104 n n 
CA CB GEK sing 105 n n 
CA HA GEK sing 106 n n 
CB CG GEK sing 107 n n 
CB HB GEK sing 108 n n 
CB HBA GEK sing 109 n n 
SD CE GEK sing 110 n n 
SD CG GEK sing 111 n n 
SD C5' GEK sing 112 n n 
CE CZ GEK sing 113 n n 
CE HE GEK sing 114 n n 
CE HEA GEK sing 115 n n 
CG HG GEK sing 116 n n 
CG HGA GEK sing 117 n n 
CZ OZ1 GEK doub 118 n n 
CZ OZ2 GEK sing 119 n n 
C1' C2' GEK sing 120 n n 
C1' O4' GEK sing 121 n n 
C1' H1' GEK sing 122 n n 
C2' O2' GEK sing 123 n n 
C2' C3' GEK sing 124 n n 
C2' H2' GEK sing 125 n n 
O2' HO2' GEK sing 126 n n 
C3' O3' GEK sing 127 n n 
C3' C4' GEK sing 128 n n 
C3' H3' GEK sing 129 n n 
O3' HO3' GEK sing 130 n n 
C4' O4' GEK sing 131 n n 
C4' C5' GEK sing 132 n n 
C4' H4' GEK sing 133 n n 
C5' H5' GEK sing 134 n n 
C5' "H5'A" GEK sing 135 n n 
N H22 GEK sing 136 n n 
#
_atom_sites.entry_id                     4QNV 
_atom_sites.fract_transf_matrix[1][1]    0.012175 
_atom_sites.fract_transf_matrix[1][2]    0.007029 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.014059 
_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]    0.002312 
_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 PO4 A 1 401 1 PO4 PO4 . 
D 3 GEK A 1 402 1 GEK GEK . 
E 2 PO4 B 1 401 2 PO4 PO4 . 
F 3 GEK B 1 402 2 GEK GEK . 
G 4 HOH A 1 501 10 HOH HOH . 
G 4 HOH A 2 502 17 HOH HOH . 
G 4 HOH A 3 503 22 HOH HOH . 
G 4 HOH A 4 504 23 HOH HOH . 
G 4 HOH A 5 505 24 HOH HOH . 
G 4 HOH A 6 506 25 HOH HOH . 
G 4 HOH A 7 507 26 HOH HOH . 
G 4 HOH A 8 508 30 HOH HOH . 
G 4 HOH A 9 509 31 HOH HOH . 
G 4 HOH A 10 510 46 HOH HOH . 
H 4 HOH B 1 501 2 HOH HOH . 
H 4 HOH B 2 502 4 HOH HOH . 
H 4 HOH B 3 503 5 HOH HOH . 
H 4 HOH B 4 504 6 HOH HOH . 
H 4 HOH B 5 505 7 HOH HOH . 
H 4 HOH B 6 506 9 HOH HOH . 
H 4 HOH B 7 507 11 HOH HOH . 
H 4 HOH B 8 508 15 HOH HOH . 
H 4 HOH B 9 509 16 HOH HOH . 
H 4 HOH B 10 510 19 HOH HOH . 
H 4 HOH B 11 511 20 HOH HOH . 
H 4 HOH B 12 512 21 HOH HOH . 
H 4 HOH B 13 513 29 HOH HOH . 
H 4 HOH B 14 514 32 HOH HOH . 
H 4 HOH B 15 515 33 HOH HOH . 
H 4 HOH B 16 516 34 HOH HOH . 
H 4 HOH B 17 517 35 HOH HOH . 
H 4 HOH B 18 518 36 HOH HOH . 
H 4 HOH B 19 519 37 HOH HOH . 
H 4 HOH B 20 520 39 HOH HOH . 
H 4 HOH B 21 521 40 HOH HOH . 
H 4 HOH B 22 522 41 HOH HOH . 
H 4 HOH B 23 523 42 HOH HOH . 
H 4 HOH B 24 524 43 HOH HOH . 
H 4 HOH B 25 525 47 HOH HOH . 
H 4 HOH B 26 526 49 HOH HOH . 
H 4 HOH B 27 527 50 HOH HOH . 
H 4 HOH B 28 528 51 HOH HOH . 
H 4 HOH B 29 529 52 HOH HOH . 
H 4 HOH B 30 530 54 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 C GEK . . . D 3 78.984 -22.44 -18.055 1 41.93 ? C GEK 402 A 1 
HETATM 2 N N GEK . . . D 3 78.093 -20.38 -17.196 1 43.29 ? N GEK 402 A 1 
HETATM 3 O O GEK . . . D 3 79.437 -23.57 -17.899 1 35.45 ? O GEK 402 A 1 
HETATM 4 N N1 GEK . . . D 3 70.92 -15.988 -11.934 1 43.16 ? N1 GEK 402 A 1 
HETATM 5 C C2 GEK . . . D 3 72.298 -16.194 -12.334 1 44.52 ? C2 GEK 402 A 1 
HETATM 6 N N3 GEK . . . D 3 72.572 -17.619 -12.329 1 47.45 ? N3 GEK 402 A 1 
HETATM 7 C C4 GEK . . . D 3 71.711 -18.556 -11.932 1 51.71 ? C4 GEK 402 A 1 
HETATM 8 C C5 GEK . . . D 3 70.51 -18.231 -11.488 1 50.72 ? C5 GEK 402 A 1 
HETATM 9 C C6 GEK . . . D 3 70.158 -16.958 -11.46 1 48.9 ? C6 GEK 402 A 1 
HETATM 10 N N6 GEK . . . D 3 68.95 -16.678 -11.005 1 55.5 ? N6 GEK 402 A 1 
HETATM 11 N N7 GEK . . . D 3 69.908 -19.352 -11.084 1 52.65 ? N7 GEK 402 A 1 
HETATM 12 C C8 GEK . . . D 3 70.731 -20.382 -11.306 1 56.83 ? C8 GEK 402 A 1 
HETATM 13 N N9 GEK . . . D 3 71.857 -19.88 -11.834 1 56.17 ? N9 GEK 402 A 1 
HETATM 14 C CA GEK . . . D 3 78.645 -21.65 -16.789 1 43.98 ? CA GEK 402 A 1 
HETATM 15 C CB GEK . . . D 3 77.639 -22.404 -15.905 1 52.78 ? CB GEK 402 A 1 
HETATM 16 S SD GEK . . . D 3 75.201 -23.697 -15.6 1 61.31 ? SD GEK 402 A 1 
HETATM 17 C CE GEK . . . D 3 74.519 -25.269 -16.325 1 71.47 ? CE GEK 402 A 1 
HETATM 18 C CG GEK . . . D 3 76.351 -22.763 -16.688 1 57.38 ? CG GEK 402 A 1 
HETATM 19 C CZ GEK . . . D 3 74.822 -25.488 -17.83 1 61.99 ? CZ GEK 402 A 1 
HETATM 20 C C1' GEK . . . D 3 73.146 -20.54 -12.253 1 52.9 ? C1' GEK 402 A 1 
HETATM 21 C C2' GEK . . . D 3 73.267 -21.947 -11.722 1 50.75 ? C2' GEK 402 A 1 
HETATM 22 O O2' GEK . . . D 3 73.652 -21.874 -10.342 1 51.9 ? O2' GEK 402 A 1 
HETATM 23 C C3' GEK . . . D 3 74.353 -22.549 -12.605 1 45.19 ? C3' GEK 402 A 1 
HETATM 24 O O3' GEK . . . D 3 75.631 -22.365 -12.017 1 40.82 ? O3' GEK 402 A 1 
HETATM 25 C C4' GEK . . . D 3 74.293 -21.723 -13.92 1 54.27 ? C4' GEK 402 A 1 
HETATM 26 O O4' GEK . . . D 3 73.325 -20.673 -13.71 1 54.57 ? O4' GEK 402 A 1 
HETATM 27 C C5' GEK . . . D 3 73.828 -22.559 -15.152 1 63.25 ? C5' GEK 402 A 1 
HETATM 28 O OXT GEK . . . D 3 78.75 -21.922 -19.161 1 52.03 ? OXT GEK 402 A 1 
HETATM 29 O OZ1 GEK . . . D 3 75.741 -26.277 -18.096 1 64.01 ? OZ1 GEK 402 A 1 
HETATM 30 O OZ2 GEK . . . D 3 74.083 -24.932 -18.683 1 53.99 ? OZ2 GEK 402 A 1 
#
_model_server_stats.io_time_ms              109 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           344 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           30 
#