data_4RH1
#
_model_server_result.job_id            dgNCoC8mzPC2SJ6fneZdMA 
_model_server_result.datetime_utc      '2024-11-20 13:21:04' 
_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          4rh1 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":402}' 
#
_entry.id    4RH1 
#
_exptl.entry_id    4RH1 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              446.34 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '[(3S)-3-amino-4-hydroxy-4-oxo-butyl]-[[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl]-methyl-selanium' 
_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            4RH1 
_cell.length_a            53.44 
_cell.length_b            58.56 
_cell.length_c            130.96 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4RH1 
_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    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_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,G,H,I,J,K 
_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                      3 
_struct_asym.id                             C 
_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
metalc ? metalc1 A SG CYS 117 A CYS 90 1_555 B FE3 SF4 . A SF4 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.113 ? 
metalc ? metalc2 A SG CYS 121 A CYS 94 1_555 B FE4 SF4 . A SF4 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.1 ? 
metalc ? metalc3 A SG CYS 124 A CYS 97 1_555 B FE1 SF4 . A SF4 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.167 ? 
metalc ? metalc4 B FE2 SF4 . A SF4 401 1_555 C O EEM . A EEM 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.971 ? 
metalc ? metalc5 B FE2 SF4 . A SF4 401 1_555 C N EEM . A EEM 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.344 ? 
#
_chem_comp.formula           'C15 H23 N6 O5 Se 1' 
_chem_comp.formula_weight    446.34 
_chem_comp.id                EEM 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '[(3S)-3-amino-4-hydroxy-4-oxo-butyl]-[[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl]-methyl-selanium' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     Se-ADENOSYLSELENOMETHIONINE 
#
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
N1 C2 EEM doub 148 n y 
C2 N3 EEM sing 149 n y 
C2 H2 EEM sing 150 n n 
C4 N3 EEM doub 151 n y 
C5 C4 EEM sing 152 n y 
N9 C4 EEM sing 153 n y 
N9 C1' EEM sing 154 n n 
C1' O4' EEM sing 155 n n 
C1' C2' EEM sing 156 n n 
C1' H1' EEM sing 157 n n 
O2' C2' EEM sing 158 n n 
C2' C3' EEM sing 159 n n 
C2' H2' EEM sing 160 n n 
C4' C3' EEM sing 161 n n 
O3' C3' EEM sing 162 n n 
C3' H3' EEM sing 163 n n 
O4' C4' EEM sing 164 n n 
C4' C5' EEM sing 165 n n 
C4' H4' EEM sing 166 n n 
C5' H5' EEM sing 167 n n 
C5' "H5'A" EEM sing 168 n n 
C5' SE EEM sing 169 n n 
C O EEM doub 170 n n 
CA C EEM sing 171 n n 
C OXT EEM sing 172 n n 
OXT HOXT EEM sing 173 n n 
CB CA EEM sing 174 n n 
N CA EEM sing 175 n n 
CA HA EEM sing 176 n n 
N HN EEM sing 177 n n 
N HNA EEM sing 178 n n 
CB CG EEM sing 179 n n 
CB HB EEM sing 180 n n 
CB HBA EEM sing 181 n n 
SE CG EEM sing 182 n n 
CG HG EEM sing 183 n n 
CG HGA EEM sing 184 n n 
SE CE EEM sing 185 n n 
CE HE EEM sing 186 n n 
CE HEA EEM sing 187 n n 
CE HEB EEM sing 188 n n 
O3' HO3' EEM sing 189 n n 
O2' HO2' EEM sing 190 n n 
C8 N9 EEM sing 191 n y 
N7 C8 EEM doub 192 n y 
C8 H8 EEM sing 193 n n 
N7 C5 EEM sing 194 n y 
C6 C5 EEM doub 195 n y 
C6 N1 EEM sing 196 n y 
N6 C6 EEM sing 197 n n 
N6 HN6 EEM sing 198 n n 
N6 HN6A EEM sing 199 n n 
#
_atom_sites.entry_id                     4RH1 
_atom_sites.fract_transf_matrix[1][1]    0.018713 
_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]    0.017077 
_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]    0.007636 
_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 SF4 A 1 401 1 SF4 SF4 . 
C 3 EEM A 1 402 1 EEM EEM . 
D 4 SO4 A 1 403 1 SO4 SO4 . 
E 4 SO4 A 1 404 3 SO4 SO4 . 
F 4 SO4 A 1 405 4 SO4 SO4 . 
G 4 SO4 A 1 406 5 SO4 SO4 . 
H 4 SO4 A 1 407 7 SO4 SO4 . 
I 4 SO4 A 1 408 9 SO4 SO4 . 
J 5 0TT A 1 409 1 0TT SP . 
K 6 HOH A 1 501 3 HOH HOH . 
K 6 HOH A 2 502 6 HOH HOH . 
K 6 HOH A 3 503 7 HOH HOH . 
K 6 HOH A 4 504 10 HOH HOH . 
K 6 HOH A 5 505 12 HOH HOH . 
K 6 HOH A 6 506 15 HOH HOH . 
K 6 HOH A 7 507 18 HOH HOH . 
K 6 HOH A 8 508 26 HOH HOH . 
K 6 HOH A 9 509 29 HOH HOH . 
K 6 HOH A 10 510 32 HOH HOH . 
K 6 HOH A 11 511 37 HOH HOH . 
K 6 HOH A 12 512 39 HOH HOH . 
K 6 HOH A 13 513 42 HOH HOH . 
K 6 HOH A 14 514 43 HOH HOH . 
K 6 HOH A 15 515 44 HOH HOH . 
K 6 HOH A 16 516 45 HOH HOH . 
K 6 HOH A 17 517 47 HOH HOH . 
K 6 HOH A 18 518 48 HOH HOH . 
K 6 HOH A 19 519 49 HOH HOH . 
K 6 HOH A 20 520 51 HOH HOH . 
K 6 HOH A 21 521 52 HOH HOH . 
K 6 HOH A 22 522 53 HOH HOH . 
K 6 HOH A 23 523 55 HOH HOH . 
K 6 HOH A 24 524 56 HOH HOH . 
K 6 HOH A 25 525 58 HOH HOH . 
K 6 HOH A 26 526 63 HOH HOH . 
K 6 HOH A 27 527 64 HOH HOH . 
K 6 HOH A 28 528 65 HOH HOH . 
K 6 HOH A 29 529 66 HOH HOH . 
K 6 HOH A 30 530 67 HOH HOH . 
K 6 HOH A 31 531 68 HOH HOH . 
K 6 HOH A 32 532 69 HOH HOH . 
K 6 HOH A 33 533 70 HOH HOH . 
K 6 HOH A 34 534 71 HOH HOH . 
K 6 HOH A 35 535 73 HOH HOH . 
K 6 HOH A 36 536 74 HOH HOH . 
K 6 HOH A 37 537 75 HOH HOH . 
K 6 HOH A 38 538 76 HOH HOH . 
K 6 HOH A 39 539 77 HOH HOH . 
K 6 HOH A 40 540 78 HOH HOH . 
K 6 HOH A 41 541 79 HOH HOH . 
K 6 HOH A 42 542 80 HOH HOH . 
K 6 HOH A 43 543 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 C2 EEM . . . C 3 -27.029 -6.901 24.688 1 32.21 ? C2 EEM 402 A 1 
HETATM 2 N N3 EEM . . . C 3 -26.766 -6.619 23.371 1 32.5 ? N3 EEM 402 A 1 
HETATM 3 C C4 EEM . . . C 3 -27.462 -5.647 22.737 1 32.78 ? C4 EEM 402 A 1 
HETATM 4 C C1' EEM . . . C 3 -26.438 -5.729 20.488 1 33.04 ? C1' EEM 402 A 1 
HETATM 5 C C2' EEM . . . C 3 -26.954 -5.758 19.066 1 33.17 ? C2' EEM 402 A 1 
HETATM 6 C C3' EEM . . . C 3 -25.687 -5.509 18.275 1 33.87 ? C3' EEM 402 A 1 
HETATM 7 C C4' EEM . . . C 3 -24.764 -4.729 19.203 1 35.19 ? C4' EEM 402 A 1 
HETATM 8 C C5' EEM . . . C 3 -24.635 -3.226 18.92 1 37.02 ? C5' EEM 402 A 1 
HETATM 9 O O EEM . . . C 3 -27.385 -4.003 15.506 1 36.44 ? O EEM 402 A 1 
HETATM 10 C C EEM . . . C 3 -26.261 -3.757 15.072 1 36.83 ? C EEM 402 A 1 
HETATM 11 O OXT EEM . . . C 3 -25.473 -4.694 14.932 1 36.6 ? OXT EEM 402 A 1 
HETATM 12 C CA EEM . . . C 3 -25.871 -2.33 14.71 1 36.81 ? CA EEM 402 A 1 
HETATM 13 N N EEM . . . C 3 -27.076 -1.471 14.572 1 36.6 ? N EEM 402 A 1 
HETATM 14 C CB EEM . . . C 3 -24.884 -1.737 15.716 1 37.79 ? CB EEM 402 A 1 
HETATM 15 C CG EEM . . . C 3 -25.462 -1.075 16.966 1 38.16 ? CG EEM 402 A 1 
HETATM 16 SE SE EEM . . . C 3 -26.233 -2.356 18.214 1 40.02 ? SE EEM 402 A 1 
HETATM 17 C CE EEM . . . C 3 -26.952 -1.116 19.524 1 41.08 ? CE EEM 402 A 1 
HETATM 18 O O4' EEM . . . C 3 -25.272 -4.925 20.509 1 34.38 ? O4' EEM 402 A 1 
HETATM 19 O O3' EEM . . . C 3 -25.094 -6.744 17.949 1 32.96 ? O3' EEM 402 A 1 
HETATM 20 O O2' EEM . . . C 3 -27.565 -7 18.78 1 31.59 ? O2' EEM 402 A 1 
HETATM 21 N N9 EEM . . . C 3 -27.395 -5.19 21.458 1 32.57 ? N9 EEM 402 A 1 
HETATM 22 C C8 EEM . . . C 3 -28.316 -4.187 21.314 1 33.09 ? C8 EEM 402 A 1 
HETATM 23 N N7 EEM . . . C 3 -28.954 -4.034 22.495 1 33.38 ? N7 EEM 402 A 1 
HETATM 24 C C5 EEM . . . C 3 -28.448 -4.92 23.383 1 33.21 ? C5 EEM 402 A 1 
HETATM 25 N N1 EEM . . . C 3 -28.01 -6.194 25.347 1 32.82 ? N1 EEM 402 A 1 
HETATM 26 C C6 EEM . . . C 3 -28.726 -5.202 24.715 1 32.6 ? C6 EEM 402 A 1 
HETATM 27 N N6 EEM . . . C 3 -29.66 -4.533 25.385 1 32.27 ? N6 EEM 402 A 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           408 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           27 
#