data_3KR1
#
_model_server_result.job_id            LIj7UEYc5WeqSV01H0XtdQ 
_model_server_result.datetime_utc      '2024-11-23 03:50:18' 
_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          3kr1 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":3001}' 
#
_entry.id    3KR1 
#
_exptl.entry_id    3KR1 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              384.411 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            S-ADENOSYL-L-HOMOCYSTEINE 
_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            3KR1 
_cell.length_a            94.054 
_cell.length_b            94.054 
_cell.length_c            189.44 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3KR1 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        96 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 43 21 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_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,G,H 
_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
? 2 C N N 
? 2 E 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
disulf ? disulf1 A SG CYS 48 A CYS 48 1_555 B SG CYS 139 B CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? 
disulf ? disulf2 A SG CYS 139 A CYS 139 1_555 B SG CYS 48 B CYS 48 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? 
#
_chem_comp.formula           'C14 H20 N6 O5 S' 
_chem_comp.formula_weight    384.411 
_chem_comp.id                SAH 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              S-ADENOSYL-L-HOMOCYSTEINE 
_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
N CA SAH sing 277 n n 
N HN1 SAH sing 278 n n 
N HN2 SAH sing 279 n n 
CA CB SAH sing 280 n n 
CA C SAH sing 281 n n 
CA HA SAH sing 282 n n 
CB CG SAH sing 283 n n 
CB HB1 SAH sing 284 n n 
CB HB2 SAH sing 285 n n 
CG SD SAH sing 286 n n 
CG HG1 SAH sing 287 n n 
CG HG2 SAH sing 288 n n 
SD C5' SAH sing 289 n n 
C O SAH doub 290 n n 
C OXT SAH sing 291 n n 
OXT HXT SAH sing 292 n n 
C5' C4' SAH sing 293 n n 
C5' "H5'1" SAH sing 294 n n 
C5' "H5'2" SAH sing 295 n n 
C4' O4' SAH sing 296 n n 
C4' C3' SAH sing 297 n n 
C4' H4' SAH sing 298 n n 
O4' C1' SAH sing 299 n n 
C3' O3' SAH sing 300 n n 
C3' C2' SAH sing 301 n n 
C3' H3' SAH sing 302 n n 
O3' HO3' SAH sing 303 n n 
C2' O2' SAH sing 304 n n 
C2' C1' SAH sing 305 n n 
C2' H2' SAH sing 306 n n 
O2' HO2' SAH sing 307 n n 
C1' N9 SAH sing 308 n n 
C1' H1' SAH sing 309 n n 
N9 C8 SAH sing 310 n y 
N9 C4 SAH sing 311 n y 
C8 N7 SAH doub 312 n y 
C8 H8 SAH sing 313 n n 
N7 C5 SAH sing 314 n y 
C5 C6 SAH sing 315 n y 
C5 C4 SAH doub 316 n y 
C6 N6 SAH sing 317 n n 
C6 N1 SAH doub 318 n y 
N6 HN61 SAH sing 319 n n 
N6 HN62 SAH sing 320 n n 
N1 C2 SAH sing 321 n y 
C2 N3 SAH doub 322 n y 
C2 H2 SAH sing 323 n n 
N3 C4 SAH sing 324 n y 
#
_atom_sites.entry_id                     3KR1 
_atom_sites.fract_transf_matrix[1][1]    0.010632 
_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]    0.010632 
_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]    0.005279 
_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 SAH A 1 3001 3001 SAH SAH . 
D 3 VGD A 1 290 1 VGD VGD . 
E 2 SAH B 1 3002 3002 SAH SAH . 
F 3 VGD B 1 290 2 VGD VGD . 
G 4 HOH A 1 291 1 HOH HOH . 
G 4 HOH A 2 292 2 HOH HOH . 
G 4 HOH A 3 293 3 HOH HOH . 
G 4 HOH A 4 294 5 HOH HOH . 
G 4 HOH A 5 295 6 HOH HOH . 
G 4 HOH A 6 296 7 HOH HOH . 
G 4 HOH A 7 297 12 HOH HOH . 
G 4 HOH A 8 298 13 HOH HOH . 
G 4 HOH A 9 299 17 HOH HOH . 
G 4 HOH A 10 300 18 HOH HOH . 
G 4 HOH A 11 301 19 HOH HOH . 
G 4 HOH A 12 302 20 HOH HOH . 
G 4 HOH A 13 303 25 HOH HOH . 
G 4 HOH A 14 304 26 HOH HOH . 
G 4 HOH A 15 305 27 HOH HOH . 
G 4 HOH A 16 306 31 HOH HOH . 
G 4 HOH A 17 307 34 HOH HOH . 
G 4 HOH A 18 308 35 HOH HOH . 
G 4 HOH A 19 309 37 HOH HOH . 
G 4 HOH A 20 310 38 HOH HOH . 
G 4 HOH A 21 311 41 HOH HOH . 
G 4 HOH A 22 312 43 HOH HOH . 
G 4 HOH A 23 313 45 HOH HOH . 
G 4 HOH A 24 314 46 HOH HOH . 
G 4 HOH A 25 315 47 HOH HOH . 
G 4 HOH A 26 316 49 HOH HOH . 
G 4 HOH A 27 317 50 HOH HOH . 
G 4 HOH A 28 318 51 HOH HOH . 
G 4 HOH A 29 319 52 HOH HOH . 
G 4 HOH A 30 320 53 HOH HOH . 
G 4 HOH A 31 321 60 HOH HOH . 
G 4 HOH A 32 322 61 HOH HOH . 
G 4 HOH A 33 323 62 HOH HOH . 
G 4 HOH A 34 324 65 HOH HOH . 
G 4 HOH A 35 325 67 HOH HOH . 
G 4 HOH A 36 326 71 HOH HOH . 
G 4 HOH A 37 327 72 HOH HOH . 
G 4 HOH A 38 328 73 HOH HOH . 
G 4 HOH A 39 329 74 HOH HOH . 
G 4 HOH A 40 330 77 HOH HOH . 
G 4 HOH A 41 331 79 HOH HOH . 
G 4 HOH A 42 332 81 HOH HOH . 
G 4 HOH A 43 333 83 HOH HOH . 
G 4 HOH A 44 334 84 HOH HOH . 
G 4 HOH A 45 335 85 HOH HOH . 
G 4 HOH A 46 336 89 HOH HOH . 
G 4 HOH A 47 337 90 HOH HOH . 
G 4 HOH A 48 338 91 HOH HOH . 
G 4 HOH A 49 339 95 HOH HOH . 
G 4 HOH A 50 340 96 HOH HOH . 
G 4 HOH A 51 341 100 HOH HOH . 
G 4 HOH A 52 342 102 HOH HOH . 
G 4 HOH A 53 343 107 HOH HOH . 
G 4 HOH A 54 344 113 HOH HOH . 
G 4 HOH A 55 345 115 HOH HOH . 
G 4 HOH A 56 346 117 HOH HOH . 
G 4 HOH A 57 347 118 HOH HOH . 
G 4 HOH A 58 348 119 HOH HOH . 
G 4 HOH A 59 349 120 HOH HOH . 
G 4 HOH A 60 350 123 HOH HOH . 
G 4 HOH A 61 351 124 HOH HOH . 
G 4 HOH A 62 352 126 HOH HOH . 
G 4 HOH A 63 353 127 HOH HOH . 
G 4 HOH A 64 354 128 HOH HOH . 
G 4 HOH A 65 355 132 HOH HOH . 
G 4 HOH A 66 356 135 HOH HOH . 
G 4 HOH A 67 357 140 HOH HOH . 
G 4 HOH A 68 358 141 HOH HOH . 
G 4 HOH A 69 359 142 HOH HOH . 
G 4 HOH A 70 360 143 HOH HOH . 
G 4 HOH A 71 361 144 HOH HOH . 
G 4 HOH A 72 362 145 HOH HOH . 
G 4 HOH A 73 363 146 HOH HOH . 
H 4 HOH B 1 291 4 HOH HOH . 
H 4 HOH B 2 292 8 HOH HOH . 
H 4 HOH B 3 293 9 HOH HOH . 
H 4 HOH B 4 294 10 HOH HOH . 
H 4 HOH B 5 295 11 HOH HOH . 
H 4 HOH B 6 296 14 HOH HOH . 
H 4 HOH B 7 297 15 HOH HOH . 
H 4 HOH B 8 298 16 HOH HOH . 
H 4 HOH B 9 299 21 HOH HOH . 
H 4 HOH B 10 300 22 HOH HOH . 
H 4 HOH B 11 301 23 HOH HOH . 
H 4 HOH B 12 302 24 HOH HOH . 
H 4 HOH B 13 303 28 HOH HOH . 
H 4 HOH B 14 304 29 HOH HOH . 
H 4 HOH B 15 305 30 HOH HOH . 
H 4 HOH B 16 306 32 HOH HOH . 
H 4 HOH B 17 307 33 HOH HOH . 
H 4 HOH B 18 308 36 HOH HOH . 
H 4 HOH B 19 309 39 HOH HOH . 
H 4 HOH B 20 310 40 HOH HOH . 
H 4 HOH B 21 311 42 HOH HOH . 
H 4 HOH B 22 312 44 HOH HOH . 
H 4 HOH B 23 313 48 HOH HOH . 
H 4 HOH B 24 314 54 HOH HOH . 
H 4 HOH B 25 315 55 HOH HOH . 
H 4 HOH B 26 316 56 HOH HOH . 
H 4 HOH B 27 317 57 HOH HOH . 
H 4 HOH B 28 318 58 HOH HOH . 
H 4 HOH B 29 319 59 HOH HOH . 
H 4 HOH B 30 320 63 HOH HOH . 
H 4 HOH B 31 321 66 HOH HOH . 
H 4 HOH B 32 322 68 HOH HOH . 
H 4 HOH B 33 323 69 HOH HOH . 
H 4 HOH B 34 324 70 HOH HOH . 
H 4 HOH B 35 325 75 HOH HOH . 
H 4 HOH B 36 326 76 HOH HOH . 
H 4 HOH B 37 327 78 HOH HOH . 
H 4 HOH B 38 328 80 HOH HOH . 
H 4 HOH B 39 329 82 HOH HOH . 
H 4 HOH B 40 330 86 HOH HOH . 
H 4 HOH B 41 331 87 HOH HOH . 
H 4 HOH B 42 332 88 HOH HOH . 
H 4 HOH B 43 333 92 HOH HOH . 
H 4 HOH B 44 334 93 HOH HOH . 
H 4 HOH B 45 335 94 HOH HOH . 
H 4 HOH B 46 336 97 HOH HOH . 
H 4 HOH B 47 337 98 HOH HOH . 
H 4 HOH B 48 338 99 HOH HOH . 
H 4 HOH B 49 339 101 HOH HOH . 
H 4 HOH B 50 340 103 HOH HOH . 
H 4 HOH B 51 341 104 HOH HOH . 
H 4 HOH B 52 342 105 HOH HOH . 
H 4 HOH B 53 343 106 HOH HOH . 
H 4 HOH B 54 344 108 HOH HOH . 
H 4 HOH B 55 345 109 HOH HOH . 
H 4 HOH B 56 346 110 HOH HOH . 
H 4 HOH B 57 347 111 HOH HOH . 
H 4 HOH B 58 348 112 HOH HOH . 
H 4 HOH B 59 349 114 HOH HOH . 
H 4 HOH B 60 350 116 HOH HOH . 
H 4 HOH B 61 351 121 HOH HOH . 
H 4 HOH B 62 352 122 HOH HOH . 
H 4 HOH B 63 353 125 HOH HOH . 
H 4 HOH B 64 354 129 HOH HOH . 
H 4 HOH B 65 355 130 HOH HOH . 
H 4 HOH B 66 356 131 HOH HOH . 
H 4 HOH B 67 357 133 HOH HOH . 
H 4 HOH B 68 358 134 HOH HOH . 
H 4 HOH B 69 359 136 HOH HOH . 
H 4 HOH B 70 360 137 HOH HOH . 
H 4 HOH B 71 361 138 HOH HOH . 
H 4 HOH B 72 362 139 HOH HOH . 
H 4 HOH B 73 363 147 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 N N SAH . . . C 2 26.333 52.803 17.638 1 47.93 ? N SAH 3001 A 1 
HETATM 2 C CA SAH . . . C 2 27.506 52.179 17.054 1 47.91 ? CA SAH 3001 A 1 
HETATM 3 C CB SAH . . . C 2 28.654 52.039 18.061 1 48.63 ? CB SAH 3001 A 1 
HETATM 4 C CG SAH . . . C 2 28.351 51.107 19.236 1 46.3 ? CG SAH 3001 A 1 
HETATM 5 S SD SAH . . . C 2 29.847 50.769 20.224 1 54.51 ? SD SAH 3001 A 1 
HETATM 6 C C SAH . . . C 2 27.133 50.854 16.388 1 47.15 ? C SAH 3001 A 1 
HETATM 7 O O SAH . . . C 2 28.032 50.21 15.968 1 46.42 ? O SAH 3001 A 1 
HETATM 8 O OXT SAH . . . C 2 25.803 50.739 15.965 1 47.09 ? OXT SAH 3001 A 1 
HETATM 9 C C5' SAH . . . C 2 29.35 51.392 21.856 1 50.95 ? C5' SAH 3001 A 1 
HETATM 10 C C4' SAH . . . C 2 29.613 52.879 22.102 1 55.42 ? C4' SAH 3001 A 1 
HETATM 11 O O4' SAH . . . C 2 29.317 53.18 23.422 1 55.19 ? O4' SAH 3001 A 1 
HETATM 12 C C3' SAH . . . C 2 31.087 53.251 21.977 1 56.05 ? C3' SAH 3001 A 1 
HETATM 13 O O3' SAH . . . C 2 31.229 54.15 20.908 1 53 ? O3' SAH 3001 A 1 
HETATM 14 C C2' SAH . . . C 2 31.386 53.864 23.178 1 54.81 ? C2' SAH 3001 A 1 
HETATM 15 O O2' SAH . . . C 2 32.254 54.96 23.035 1 52.51 ? O2' SAH 3001 A 1 
HETATM 16 C C1' SAH . . . C 2 30.124 54.266 23.693 1 56.14 ? C1' SAH 3001 A 1 
HETATM 17 N N9 SAH . . . C 2 30.116 54.541 25.121 1 58.65 ? N9 SAH 3001 A 1 
HETATM 18 C C8 SAH . . . C 2 30.968 54.075 26.03 1 57.6 ? C8 SAH 3001 A 1 
HETATM 19 N N7 SAH . . . C 2 30.578 54.544 27.269 1 59.22 ? N7 SAH 3001 A 1 
HETATM 20 C C5 SAH . . . C 2 29.46 55.306 27.093 1 59.99 ? C5 SAH 3001 A 1 
HETATM 21 C C6 SAH . . . C 2 28.674 56.001 27.968 1 61.55 ? C6 SAH 3001 A 1 
HETATM 22 N N6 SAH . . . C 2 28.985 55.999 29.385 1 65.66 ? N6 SAH 3001 A 1 
HETATM 23 N N1 SAH . . . C 2 27.616 56.678 27.528 1 61.37 ? N1 SAH 3001 A 1 
HETATM 24 C C2 SAH . . . C 2 27.319 56.683 26.211 1 61.78 ? C2 SAH 3001 A 1 
HETATM 25 N N3 SAH . . . C 2 28.102 55.994 25.343 1 60.04 ? N3 SAH 3001 A 1 
HETATM 26 C C4 SAH . . . C 2 29.164 55.313 25.788 1 60.17 ? C4 SAH 3001 A 1 
#
_model_server_stats.io_time_ms              13 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           301 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           26 
#