data_5M2X
#
_model_server_result.job_id            lbB6FD-EFuT8cTRlWdXaIA 
_model_server_result.datetime_utc      '2024-11-17 06:41:19' 
_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          5m2x 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"FA","auth_seq_id":1001}' 
#
_entry.id    5M2X 
#
_exptl.entry_id    5M2X 
_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    6 
_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            5M2X 
_cell.length_a            191.06 
_cell.length_b            192.06 
_cell.length_c            407.23 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5M2X 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
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 3 1 
D,T,U,V,W,X,Y,Z 4 1 
E,AA,BA,CA,DA,EA 5 1 
F,FA,GA,HA,IA,JA,KA,LA 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
? 2 G N N 
? 2 L N N 
? 2 P N N 
? 2 T N N 
? 2 AA N N 
? 2 FA 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
metalc ? metalc1 A OE2 GLU 440 A GLU 439 1_555 K ZN ZN . A ZN 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.091 ? 
metalc ? metalc2 A NE2 HIS 444 A HIS 443 1_555 K ZN ZN . A ZN 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.142 ? 
metalc ? metalc3 A SG CYS 449 A CYS 448 1_555 K ZN ZN . A ZN 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.466 ? 
metalc ? metalc4 A SG CYS 452 A CYS 451 1_555 K ZN ZN . A ZN 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.421 ? 
metalc ? metalc5 A NE2 HIS 715 A HIS 714 1_555 J ZN ZN . A ZN 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.578 ? 
metalc ? metalc6 A SG CYS 731 A CYS 730 1_555 J ZN ZN . A ZN 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.452 ? 
metalc ? metalc7 A SG CYS 850 A CYS 849 1_555 J ZN ZN . A ZN 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.386 ? 
metalc ? metalc8 B NE2 HIS 715 B HIS 714 1_555 O ZN ZN . B ZN 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.529 ? 
metalc ? metalc9 B SG CYS 731 B CYS 730 1_555 O ZN ZN . B ZN 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.64 ? 
metalc ? metalc10 B SG CYS 850 B CYS 849 1_555 O ZN ZN . B ZN 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.311 ? 
metalc ? metalc11 C OE2 GLU 440 C GLU 439 1_555 S ZN ZN . C ZN 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.987 ? 
metalc ? metalc12 C NE2 HIS 444 C HIS 443 1_555 S ZN ZN . C ZN 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.085 ? 
metalc ? metalc13 C SG CYS 449 C CYS 448 1_555 S ZN ZN . C ZN 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.37 ? 
metalc ? metalc14 C SG CYS 452 C CYS 451 1_555 S ZN ZN . C ZN 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.453 ? 
metalc ? metalc15 C SG CYS 731 C CYS 730 1_555 R ZN ZN . C ZN 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.671 ? 
metalc ? metalc16 C SG CYS 850 C CYS 849 1_555 R ZN ZN . C ZN 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.379 ? 
metalc ? metalc17 D OE2 GLU 440 D GLU 439 1_555 Z ZN ZN . D ZN 1007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.916 ? 
metalc ? metalc18 D SG CYS 449 D CYS 448 1_555 Z ZN ZN . D ZN 1007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.609 ? 
metalc ? metalc19 D SG CYS 452 D CYS 451 1_555 Z ZN ZN . D ZN 1007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.315 ? 
metalc ? metalc20 D NE2 HIS 715 D HIS 714 1_555 Y ZN ZN . D ZN 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? 
metalc ? metalc21 D SG CYS 731 D CYS 730 1_555 Y ZN ZN . D ZN 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.311 ? 
metalc ? metalc22 D SG CYS 850 D CYS 849 1_555 Y ZN ZN . D ZN 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.369 ? 
metalc ? metalc23 E OE2 GLU 440 E GLU 439 1_555 EA ZN ZN . E ZN 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? 
metalc ? metalc24 E NE2 HIS 444 E HIS 443 1_555 EA ZN ZN . E ZN 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.148 ? 
metalc ? metalc25 E SG CYS 449 E CYS 448 1_555 EA ZN ZN . E ZN 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.378 ? 
metalc ? metalc26 E SG CYS 452 E CYS 451 1_555 EA ZN ZN . E ZN 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.369 ? 
metalc ? metalc27 E NE2 HIS 715 E HIS 714 1_555 DA ZN ZN . E ZN 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.128 ? 
metalc ? metalc28 E SG CYS 731 E CYS 730 1_555 DA ZN ZN . E ZN 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.345 ? 
metalc ? metalc29 E SG CYS 850 E CYS 849 1_555 DA ZN ZN . E ZN 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.378 ? 
metalc ? metalc30 F OE2 GLU 440 F GLU 439 1_555 LA ZN ZN . F ZN 1007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? 
metalc ? metalc31 F NE2 HIS 444 F HIS 443 1_555 LA ZN ZN . F ZN 1007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.464 ? 
metalc ? metalc32 F SG CYS 449 F CYS 448 1_555 LA ZN ZN . F ZN 1007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.386 ? 
metalc ? metalc33 F SG CYS 452 F CYS 451 1_555 LA ZN ZN . F ZN 1007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.332 ? 
metalc ? metalc34 F SG CYS 850 F CYS 849 1_555 KA ZN ZN . F ZN 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.391 ? 
#
_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                     5M2X 
_atom_sites.fract_transf_matrix[1][1]    0.005234 
_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]    0.005207 
_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]    0.002456 
_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 SAH A 1 1001 1 SAH SAH . 
H 3 PO4 A 1 1002 3 PO4 PO4 . 
I 3 PO4 A 1 1003 4 PO4 PO4 . 
J 4 ZN A 1 1004 3 ZN ZN . 
K 4 ZN A 1 1005 11 ZN ZN . 
L 2 SAH B 1 1001 2 SAH SAH . 
M 3 PO4 B 1 1002 1 PO4 PO4 . 
N 3 PO4 B 1 1003 5 PO4 PO4 . 
O 4 ZN B 1 1004 4 ZN ZN . 
P 2 SAH C 1 1001 3 SAH SAH . 
Q 3 PO4 C 1 1002 6 PO4 PO4 . 
R 4 ZN C 1 1003 5 ZN ZN . 
S 4 ZN C 1 1004 7 ZN ZN . 
T 2 SAH D 1 1001 4 SAH SAH . 
U 3 PO4 D 1 1002 7 PO4 PO4 . 
V 3 PO4 D 1 1003 8 PO4 PO4 . 
W 3 PO4 D 1 1004 9 PO4 PO4 . 
X 3 PO4 D 1 1005 10 PO4 PO4 . 
Y 4 ZN D 1 1006 1 ZN ZN . 
Z 4 ZN D 1 1007 8 ZN ZN . 
AA 2 SAH E 1 1001 5 SAH SAH . 
BA 3 PO4 E 1 1002 2 PO4 PO4 . 
CA 3 PO4 E 1 1003 11 PO4 PO4 . 
DA 4 ZN E 1 1004 2 ZN ZN . 
EA 4 ZN E 1 1005 9 ZN ZN . 
FA 2 SAH F 1 1001 6 SAH SAH . 
GA 3 PO4 F 1 1002 12 PO4 PO4 . 
HA 3 PO4 F 1 1003 13 PO4 PO4 . 
IA 3 PO4 F 1 1004 14 PO4 PO4 . 
JA 3 PO4 F 1 1005 15 PO4 PO4 . 
KA 4 ZN F 1 1006 6 ZN ZN . 
LA 4 ZN F 1 1007 10 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 . . . FA 2 -37.033 45.733 -3.268 1 126.33 ? N SAH 1001 F 1 
HETATM 2 C CA SAH . . . FA 2 -38.165 46.699 -3.248 1 140.2 ? CA SAH 1001 F 1 
HETATM 3 C CB SAH . . . FA 2 -37.741 48.012 -3.894 1 138.34 ? CB SAH 1001 F 1 
HETATM 4 C CG SAH . . . FA 2 -37.254 49.005 -2.844 1 128.59 ? CG SAH 1001 F 1 
HETATM 5 S SD SAH . . . FA 2 -36.267 50.243 -3.618 1 199.43 ? SD SAH 1001 F 1 
HETATM 6 C C SAH . . . FA 2 -39.367 46.155 -3.961 1 119.67 ? C SAH 1001 F 1 
HETATM 7 O O SAH . . . FA 2 -39.201 45.586 -5.062 1 114.38 ? O SAH 1001 F 1 
HETATM 8 O OXT SAH . . . FA 2 -40.49 46.292 -3.428 1 102.42 ? OXT SAH 1001 F 1 
HETATM 9 C C5' SAH . . . FA 2 -36.993 51.825 -3.349 1 170.31 ? C5' SAH 1001 F 1 
HETATM 10 C C4' SAH . . . FA 2 -38.119 52.045 -4.352 1 159.18 ? C4' SAH 1001 F 1 
HETATM 11 O O4' SAH . . . FA 2 -39.24 52.643 -3.695 1 144.93 ? O4' SAH 1001 F 1 
HETATM 12 C C3' SAH . . . FA 2 -37.683 52.972 -5.477 1 157.33 ? C3' SAH 1001 F 1 
HETATM 13 O O3' SAH . . . FA 2 -37.696 52.256 -6.72 1 155.41 ? O3' SAH 1001 F 1 
HETATM 14 C C2' SAH . . . FA 2 -38.638 54.162 -5.438 1 147.1 ? C2' SAH 1001 F 1 
HETATM 15 O O2' SAH . . . FA 2 -39.365 54.367 -6.659 1 150.27 ? O2' SAH 1001 F 1 
HETATM 16 C C1' SAH . . . FA 2 -39.615 53.882 -4.304 1 139.75 ? C1' SAH 1001 F 1 
HETATM 17 N N9 SAH . . . FA 2 -39.546 54.975 -3.302 1 140.4 ? N9 SAH 1001 F 1 
HETATM 18 C C8 SAH . . . FA 2 -38.423 55.455 -2.736 1 142.37 ? C8 SAH 1001 F 1 
HETATM 19 N N7 SAH . . . FA 2 -38.703 56.454 -1.861 1 145.23 ? N7 SAH 1001 F 1 
HETATM 20 C C5 SAH . . . FA 2 -40.038 56.626 -1.858 1 144.13 ? C5 SAH 1001 F 1 
HETATM 21 C C6 SAH . . . FA 2 -40.999 57.513 -1.163 1 141.29 ? C6 SAH 1001 F 1 
HETATM 22 N N6 SAH . . . FA 2 -40.577 58.441 -0.27 1 144.72 ? N6 SAH 1001 F 1 
HETATM 23 N N1 SAH . . . FA 2 -42.312 57.365 -1.449 1 138.06 ? N1 SAH 1001 F 1 
HETATM 24 C C2 SAH . . . FA 2 -42.745 56.448 -2.333 1 138.42 ? C2 SAH 1001 F 1 
HETATM 25 N N3 SAH . . . FA 2 -41.929 55.611 -3 1 136.55 ? N3 SAH 1001 F 1 
HETATM 26 C C4 SAH . . . FA 2 -40.589 55.649 -2.81 1 140.45 ? C4 SAH 1001 F 1 
#
_model_server_stats.io_time_ms              17 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    39 
_model_server_stats.query_time_ms           215 
_model_server_stats.encode_time_ms          28 
_model_server_stats.element_count           26 
#