data_5M2Z
#
_model_server_result.job_id            lXY5r_GhOeiCSclUf6IBMw 
_model_server_result.datetime_utc      '2024-11-17 08:18:41' 
_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          5m2z 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"CA","auth_seq_id":1005}' 
#
_entry.id    5M2Z 
#
_exptl.entry_id    5M2Z 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              384.411 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            S-ADENOSYL-L-HOMOCYSTEINE 
_entity.pdbx_number_of_molecules    3 
_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            5M2Z 
_cell.length_a            234.578 
_cell.length_b            234.578 
_cell.length_c            406.123 
_cell.Z_PDB               36 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5M2Z 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        170 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 65' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? monomeric 1 author_defined_assembly 1 
? monomeric 1 author_defined_assembly 2 
? monomeric 1 author_defined_assembly 3 
? monomeric 1 author_defined_assembly 4 
? monomeric 1 author_defined_assembly 5 
? monomeric 1 author_defined_assembly 6 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,G,H,I,J,K 1 1 
B,L,M,N,O 2 1 
C,P,Q,R,S,T 3 1 
D,U,V,W,X 4 1 
E,Y,Z,AA,BA,CA,DA,EA 5 1 
F,FA,GA,HA,IA,JA,KA 6 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
? 4 N N N 
? 4 CA N N 
? 4 IA 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
covale ? covale1 E NZ LYS 77 E LYS 76 1_555 BA O3 PO4 . E PO4 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.294 ? 
metalc ? metalc1 A OE2 GLU 440 A GLU 439 1_555 K ZN ZN . A ZN 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.939 ? 
metalc ? metalc2 A NE2 HIS 444 A HIS 443 1_555 K ZN ZN . A ZN 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? 
metalc ? metalc3 A SG CYS 449 A CYS 448 1_555 K ZN ZN . A ZN 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.427 ? 
metalc ? metalc4 A SG CYS 452 A CYS 451 1_555 K ZN ZN . A ZN 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.379 ? 
metalc ? metalc5 A NE2 HIS 715 A HIS 714 1_555 J ZN ZN . A ZN 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? 
metalc ? metalc6 A SG CYS 731 A CYS 730 1_555 J ZN ZN . A ZN 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.39 ? 
metalc ? metalc7 A SG CYS 850 A CYS 849 1_555 J ZN ZN . A ZN 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.384 ? 
metalc ? metalc8 B NE2 HIS 715 C HIS 714 1_555 O ZN ZN . C ZN 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.231 ? 
metalc ? metalc9 B SG CYS 731 C CYS 730 1_555 O ZN ZN . C ZN 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.464 ? 
metalc ? metalc10 B SG CYS 850 C CYS 849 1_555 O ZN ZN . C ZN 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.367 ? 
metalc ? metalc11 C NE2 HIS 444 B HIS 443 1_555 T ZN ZN . B ZN 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.237 ? 
metalc ? metalc12 C SG CYS 449 B CYS 448 1_555 T ZN ZN . B ZN 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.296 ? 
metalc ? metalc13 C SG CYS 452 B CYS 451 1_555 T ZN ZN . B ZN 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.313 ? 
metalc ? metalc14 C NE2 HIS 715 B HIS 714 1_555 S ZN ZN . B ZN 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.083 ? 
metalc ? metalc15 C SG CYS 731 B CYS 730 1_555 S ZN ZN . B ZN 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.418 ? 
metalc ? metalc16 C SG CYS 850 B CYS 849 1_555 S ZN ZN . B ZN 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.346 ? 
metalc ? metalc17 D OE2 GLU 440 D GLU 439 1_555 X ZN ZN . D ZN 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.948 ? 
metalc ? metalc18 D NE2 HIS 444 D HIS 443 1_555 X ZN ZN . D ZN 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? 
metalc ? metalc19 D SG CYS 449 D CYS 448 1_555 X ZN ZN . D ZN 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.39 ? 
metalc ? metalc20 D SG CYS 452 D CYS 451 1_555 X ZN ZN . D ZN 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.384 ? 
metalc ? metalc21 D NE2 HIS 715 D HIS 714 1_555 W ZN ZN . D ZN 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.242 ? 
metalc ? metalc22 D SG CYS 850 D CYS 849 1_555 W ZN ZN . D ZN 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.359 ? 
metalc ? metalc23 E OE2 GLU 440 E GLU 439 1_555 EA ZN ZN . E ZN 1007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.91 ? 
metalc ? metalc24 E NE2 HIS 444 E HIS 443 1_555 EA ZN ZN . E ZN 1007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.235 ? 
metalc ? metalc25 E SG CYS 449 E CYS 448 1_555 EA ZN ZN . E ZN 1007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.402 ? 
metalc ? metalc26 E SG CYS 452 E CYS 451 1_555 EA ZN ZN . E ZN 1007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.349 ? 
metalc ? metalc27 E NE2 HIS 715 E HIS 714 1_555 DA ZN ZN . E ZN 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? 
metalc ? metalc28 E SG CYS 731 E CYS 730 1_555 DA ZN ZN . E ZN 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.558 ? 
metalc ? metalc29 E SG CYS 850 E CYS 849 1_555 DA ZN ZN . E ZN 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.375 ? 
metalc ? metalc30 F OE2 GLU 440 F GLU 439 1_555 KA ZN ZN . F ZN 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.921 ? 
metalc ? metalc31 F NE2 HIS 444 F HIS 443 1_555 KA ZN ZN . F ZN 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.131 ? 
metalc ? metalc32 F SG CYS 449 F CYS 448 1_555 KA ZN ZN . F ZN 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.499 ? 
metalc ? metalc33 F SG CYS 452 F CYS 451 1_555 KA ZN ZN . F ZN 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.34 ? 
metalc ? metalc34 F NE2 HIS 715 F HIS 714 1_555 JA ZN ZN . F ZN 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.007 ? 
metalc ? metalc35 F SG CYS 731 F CYS 730 1_555 JA ZN ZN . F ZN 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.473 ? 
metalc ? metalc36 F SG CYS 850 F CYS 849 1_555 JA ZN ZN . F ZN 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.333 ? 
#
_chem_comp.formula           'C14 H20 N6 O5 S' 
_chem_comp.formula_weight    384.411 
_chem_comp.id                SAH 
_chem_comp.mon_nstd_flag     n 
_chem_comp.name              S-ADENOSYL-L-HOMOCYSTEINE 
_chem_comp.type              'l-peptide linking' 
_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 279 n n 
N HN1 SAH sing 280 n n 
N HN2 SAH sing 281 n n 
CA CB SAH sing 282 n n 
CA C SAH sing 283 n n 
CA HA SAH sing 284 n n 
CB CG SAH sing 285 n n 
CB HB1 SAH sing 286 n n 
CB HB2 SAH sing 287 n n 
CG SD SAH sing 288 n n 
CG HG1 SAH sing 289 n n 
CG HG2 SAH sing 290 n n 
SD C5' SAH sing 291 n n 
C O SAH doub 292 n n 
C OXT SAH sing 293 n n 
OXT HXT SAH sing 294 n n 
C5' C4' SAH sing 295 n n 
C5' "H5'1" SAH sing 296 n n 
C5' "H5'2" SAH sing 297 n n 
C4' O4' SAH sing 298 n n 
C4' C3' SAH sing 299 n n 
C4' H4' SAH sing 300 n n 
O4' C1' SAH sing 301 n n 
C3' O3' SAH sing 302 n n 
C3' C2' SAH sing 303 n n 
C3' H3' SAH sing 304 n n 
O3' HO3' SAH sing 305 n n 
C2' O2' SAH sing 306 n n 
C2' C1' SAH sing 307 n n 
C2' H2' SAH sing 308 n n 
O2' HO2' SAH sing 309 n n 
C1' N9 SAH sing 310 n n 
C1' H1' SAH sing 311 n n 
N9 C8 SAH sing 312 n y 
N9 C4 SAH sing 313 n y 
C8 N7 SAH doub 314 n y 
C8 H8 SAH sing 315 n n 
N7 C5 SAH sing 316 n y 
C5 C6 SAH sing 317 n y 
C5 C4 SAH doub 318 n y 
C6 N6 SAH sing 319 n n 
C6 N1 SAH doub 320 n y 
N6 HN61 SAH sing 321 n n 
N6 HN62 SAH sing 322 n n 
N1 C2 SAH sing 323 n y 
C2 N3 SAH doub 324 n y 
C2 H2 SAH sing 325 n n 
N3 C4 SAH sing 326 n y 
#
_atom_sites.entry_id                     5M2Z 
_atom_sites.fract_transf_matrix[1][1]    0.004263 
_atom_sites.fract_transf_matrix[1][2]    0.002461 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.004922 
_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]    0.002462 
_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
G 2 PO4 A 1 1001 1 PO4 PO4 . 
H 2 PO4 A 1 1002 3 PO4 PO4 . 
I 2 PO4 A 1 1003 9 PO4 PO4 . 
J 3 ZN A 1 1004 3 ZN ZN . 
K 3 ZN A 1 1005 4 ZN ZN . 
L 2 PO4 C 1 1001 4 PO4 PO4 . 
M 2 PO4 C 1 1002 12 PO4 PO4 . 
N 4 SAH C 1 1003 1 SAH SAH . 
O 3 ZN C 1 1004 7 ZN ZN . 
P 2 PO4 B 1 1001 2 PO4 PO4 . 
Q 2 PO4 B 1 1002 10 PO4 PO4 . 
R 2 PO4 B 1 1003 11 PO4 PO4 . 
S 3 ZN B 1 1004 5 ZN ZN . 
T 3 ZN B 1 1005 6 ZN ZN . 
U 2 PO4 D 1 1001 13 PO4 PO4 . 
V 2 PO4 D 1 1002 14 PO4 PO4 . 
W 3 ZN D 1 1003 1 ZN ZN . 
X 3 ZN D 1 1004 8 ZN ZN . 
Y 2 PO4 E 1 1001 8 PO4 PO4 . 
Z 2 PO4 E 1 1002 15 PO4 PO4 . 
AA 2 PO4 E 1 1003 16 PO4 PO4 . 
BA 2 PO4 E 1 1004 17 PO4 PO4 . 
CA 4 SAH E 1 1005 2 SAH SAH . 
DA 3 ZN E 1 1006 9 ZN ZN . 
EA 3 ZN E 1 1007 10 ZN ZN . 
FA 2 PO4 F 1 1001 7 PO4 PO4 . 
GA 2 PO4 F 1 1002 18 PO4 PO4 . 
HA 2 PO4 F 1 1003 19 PO4 PO4 . 
IA 4 SAH F 1 1004 3 SAH SAH . 
JA 3 ZN F 1 1005 2 ZN ZN . 
KA 3 ZN F 1 1006 11 ZN ZN . 
#
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 . . . CA 4 142.089 163.36 21.055 1 195.9 ? N SAH 1005 E 1 
HETATM 2 C CA SAH . . . CA 4 141.877 163.301 22.494 1 206.26 ? CA SAH 1005 E 1 
HETATM 3 C CB SAH . . . CA 4 140.425 162.953 22.807 1 219.8 ? CB SAH 1005 E 1 
HETATM 4 C CG SAH . . . CA 4 139.423 163.308 21.712 1 219.8 ? CG SAH 1005 E 1 
HETATM 5 S SD SAH . . . CA 4 137.72 163.278 22.329 1 263.91 ? SD SAH 1005 E 1 
HETATM 6 C C SAH . . . CA 4 142.825 162.31 23.161 1 198.47 ? C SAH 1005 E 1 
HETATM 7 O O SAH . . . CA 4 143.867 161.956 22.61 1 185.12 ? O SAH 1005 E 1 
HETATM 8 O OXT SAH . . . CA 4 142.582 161.856 24.278 1 209.08 ? OXT SAH 1005 E 1 
HETATM 9 C C5' SAH . . . CA 4 137.381 164.908 21.613 1 223.81 ? C5' SAH 1005 E 1 
HETATM 10 C C4' SAH . . . CA 4 137.551 166.049 22.612 1 222.86 ? C4' SAH 1005 E 1 
HETATM 11 O O4' SAH . . . CA 4 137.532 167.289 21.932 1 212.67 ? O4' SAH 1005 E 1 
HETATM 12 C C3' SAH . . . CA 4 136.44 166.108 23.651 1 229.03 ? C3' SAH 1005 E 1 
HETATM 13 O O3' SAH . . . CA 4 136.887 165.606 24.889 1 227.54 ? O3' SAH 1005 E 1 
HETATM 14 C C2' SAH . . . CA 4 136.1 167.579 23.781 1 224.07 ? C2' SAH 1005 E 1 
HETATM 15 O O2' SAH . . . CA 4 136.406 168.031 25.08 1 220.93 ? O2' SAH 1005 E 1 
HETATM 16 C C1' SAH . . . CA 4 136.971 168.291 22.755 1 218.78 ? C1' SAH 1005 E 1 
HETATM 17 N N9 SAH . . . CA 4 136.151 169.223 21.955 1 219.28 ? N9 SAH 1005 E 1 
HETATM 18 C C8 SAH . . . CA 4 134.833 169.056 21.62 1 217.85 ? C8 SAH 1005 E 1 
HETATM 19 N N7 SAH . . . CA 4 134.433 170.122 20.888 1 214.27 ? N7 SAH 1005 E 1 
HETATM 20 C C5 SAH . . . CA 4 135.474 170.973 20.749 1 215.26 ? C5 SAH 1005 E 1 
HETATM 21 C C6 SAH . . . CA 4 135.612 172.199 20.102 1 213.43 ? C6 SAH 1005 E 1 
HETATM 22 N N6 SAH . . . CA 4 134.586 172.748 19.457 1 212.44 ? N6 SAH 1005 E 1 
HETATM 23 N N1 SAH . . . CA 4 136.826 172.853 20.131 1 210.54 ? N1 SAH 1005 E 1 
HETATM 24 C C2 SAH . . . CA 4 137.893 172.288 20.798 1 209.69 ? C2 SAH 1005 E 1 
HETATM 25 N N3 SAH . . . CA 4 137.75 171.072 21.437 1 215 ? N3 SAH 1005 E 1 
HETATM 26 C C4 SAH . . . CA 4 136.561 170.421 21.417 1 216.61 ? C4 SAH 1005 E 1 
#
_model_server_stats.io_time_ms              52 
_model_server_stats.parse_time_ms           18 
_model_server_stats.create_model_time_ms    355 
_model_server_stats.query_time_ms           282 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           26 
#