data_6KR3
#
_model_server_result.job_id            Tk_xVRRIcAEnrNY3XnNN6w 
_model_server_result.datetime_utc      '2025-08-28 04:44:44' 
_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          6kr3 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"P","auth_seq_id":1014}' 
#
_entry.id    6KR3 
#
_exptl.entry_id    6KR3 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              384.411 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            S-ADENOSYL-L-HOMOCYSTEINE 
_entity.pdbx_number_of_molecules    4 
_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            6KR3 
_cell.length_a            178.845 
_cell.length_b            209.975 
_cell.length_c            157.873 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6KR3 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        20 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 2 2 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 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,EA 1 1 
B,U,V,W,X,Y,Z,AA,BA,CA,DA,FA 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 O N N 
? 3 P N N 
? 3 X N N 
? 3 Y 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 NE2 HIS 443 A HIS 442 1_555 Q ZN ZN . A ZN 1015 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? 
metalc ? metalc2 A SG CYS 448 A CYS 447 1_555 Q ZN ZN . A ZN 1015 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? 
metalc ? metalc3 A SG CYS 451 A CYS 450 1_555 Q ZN ZN . A ZN 1015 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.906 ? 
metalc ? metalc4 A NE2 HIS 713 A HIS 712 1_555 R ZN ZN . A ZN 1016 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.761 ? 
metalc ? metalc5 A NE2 HIS 715 A HIS 714 1_555 R ZN ZN . A ZN 1016 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? 
metalc ? metalc6 A SG CYS 729 A CYS 728 1_555 R ZN ZN . A ZN 1016 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.108 ? 
metalc ? metalc7 A SG CYS 848 A CYS 847 1_555 R ZN ZN . A ZN 1016 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.925 ? 
metalc ? metalc8 B NE2 HIS 443 B HIS 442 1_555 Z ZN ZN . B ZN 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? 
metalc ? metalc9 B SG CYS 451 B CYS 450 1_555 Z ZN ZN . B ZN 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? 
metalc ? metalc10 B NE2 HIS 713 B HIS 712 1_555 AA ZN ZN . B ZN 1007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.741 ? 
metalc ? metalc11 B NE2 HIS 715 B HIS 714 1_555 AA ZN ZN . B ZN 1007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.76 ? 
metalc ? metalc12 B SG CYS 729 B CYS 728 1_555 AA ZN ZN . B ZN 1007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.181 ? 
metalc ? metalc13 B SG CYS 848 B CYS 847 1_555 AA ZN ZN . B ZN 1007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.966 ? 
#
_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 290 n n 
N HN1 SAH sing 291 n n 
N HN2 SAH sing 292 n n 
CA CB SAH sing 293 n n 
CA C SAH sing 294 n n 
CA HA SAH sing 295 n n 
CB CG SAH sing 296 n n 
CB HB1 SAH sing 297 n n 
CB HB2 SAH sing 298 n n 
CG SD SAH sing 299 n n 
CG HG1 SAH sing 300 n n 
CG HG2 SAH sing 301 n n 
SD C5' SAH sing 302 n n 
C O SAH doub 303 n n 
C OXT SAH sing 304 n n 
OXT HXT SAH sing 305 n n 
C5' C4' SAH sing 306 n n 
C5' "H5'1" SAH sing 307 n n 
C5' "H5'2" SAH sing 308 n n 
C4' O4' SAH sing 309 n n 
C4' C3' SAH sing 310 n n 
C4' H4' SAH sing 311 n n 
O4' C1' SAH sing 312 n n 
C3' O3' SAH sing 313 n n 
C3' C2' SAH sing 314 n n 
C3' H3' SAH sing 315 n n 
O3' HO3' SAH sing 316 n n 
C2' O2' SAH sing 317 n n 
C2' C1' SAH sing 318 n n 
C2' H2' SAH sing 319 n n 
O2' HO2' SAH sing 320 n n 
C1' N9 SAH sing 321 n n 
C1' H1' SAH sing 322 n n 
N9 C8 SAH sing 323 n y 
N9 C4 SAH sing 324 n y 
C8 N7 SAH doub 325 n y 
C8 H8 SAH sing 326 n n 
N7 C5 SAH sing 327 n y 
C5 C6 SAH sing 328 n y 
C5 C4 SAH doub 329 n y 
C6 N6 SAH sing 330 n n 
C6 N1 SAH doub 331 n y 
N6 HN61 SAH sing 332 n n 
N6 HN62 SAH sing 333 n n 
N1 C2 SAH sing 334 n y 
C2 N3 SAH doub 335 n y 
C2 H2 SAH sing 336 n n 
N3 C4 SAH sing 337 n y 
#
_atom_sites.entry_id                     6KR3 
_atom_sites.fract_transf_matrix[1][1]    0.005591 
_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]    0.004762 
_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]    0.006334 
_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 IOD A 1 1001 501 IOD IOD . 
D 2 IOD A 1 1002 502 IOD IOD . 
E 2 IOD A 1 1003 503 IOD IOD . 
F 2 IOD A 1 1004 504 IOD IOD . 
G 2 IOD A 1 1005 505 IOD IOD . 
H 2 IOD A 1 1006 506 IOD IOD . 
I 2 IOD A 1 1007 509 IOD IOD . 
J 2 IOD A 1 1008 510 IOD IOD . 
K 2 IOD A 1 1009 512 IOD IOD . 
L 2 IOD A 1 1010 517 IOD IOD . 
M 2 IOD A 1 1011 518 IOD IOD . 
N 2 IOD A 1 1012 520 IOD IOD . 
O 3 SAH A 1 1013 1001 SAH SAH . 
P 3 SAH A 1 1014 1011 SAH SAH . 
Q 4 ZN A 1 1015 2001 ZN ZN . 
R 4 ZN A 1 1016 2002 ZN ZN . 
S 5 GOL A 1 1017 128 GOL GOL . 
T 5 GOL A 1 1018 129 GOL GOL . 
U 2 IOD B 1 1001 507 IOD IOD . 
V 2 IOD B 1 1002 508 IOD IOD . 
W 2 IOD B 1 1003 514 IOD IOD . 
X 3 SAH B 1 1004 1031 SAH SAH . 
Y 3 SAH B 1 1005 1041 SAH SAH . 
Z 4 ZN B 1 1006 2003 ZN ZN . 
AA 4 ZN B 1 1007 2004 ZN ZN . 
BA 5 GOL B 1 1008 125 GOL GOL . 
CA 5 GOL B 1 1009 126 GOL GOL . 
DA 5 GOL B 1 1010 130 GOL GOL . 
EA 6 HOH A 1 1101 5 HOH HOH . 
EA 6 HOH A 2 1102 10 HOH HOH . 
EA 6 HOH A 3 1103 46 HOH HOH . 
EA 6 HOH A 4 1104 16 HOH HOH . 
EA 6 HOH A 5 1105 7 HOH HOH . 
EA 6 HOH A 6 1106 44 HOH HOH . 
EA 6 HOH A 7 1107 9 HOH HOH . 
EA 6 HOH A 8 1108 34 HOH HOH . 
EA 6 HOH A 9 1109 42 HOH HOH . 
EA 6 HOH A 10 1110 45 HOH HOH . 
EA 6 HOH A 11 1111 3 HOH HOH . 
EA 6 HOH A 12 1112 14 HOH HOH . 
EA 6 HOH A 13 1113 4 HOH HOH . 
EA 6 HOH A 14 1114 15 HOH HOH . 
EA 6 HOH A 15 1115 43 HOH HOH . 
EA 6 HOH A 16 1116 41 HOH HOH . 
EA 6 HOH A 17 1117 39 HOH HOH . 
EA 6 HOH A 18 1118 32 HOH HOH . 
EA 6 HOH A 19 1119 47 HOH HOH . 
EA 6 HOH A 20 1120 2 HOH HOH . 
EA 6 HOH A 21 1121 6 HOH HOH . 
EA 6 HOH A 22 1122 18 HOH HOH . 
EA 6 HOH A 23 1123 31 HOH HOH . 
EA 6 HOH A 24 1124 13 HOH HOH . 
EA 6 HOH A 25 1125 49 HOH HOH . 
EA 6 HOH A 26 1126 17 HOH HOH . 
EA 6 HOH A 27 1127 11 HOH HOH . 
EA 6 HOH A 28 1128 38 HOH HOH . 
EA 6 HOH A 29 1129 35 HOH HOH . 
EA 6 HOH A 30 1130 37 HOH HOH . 
EA 6 HOH A 31 1131 36 HOH HOH . 
FA 6 HOH B 1 1101 27 HOH HOH . 
FA 6 HOH B 2 1102 40 HOH HOH . 
FA 6 HOH B 3 1103 28 HOH HOH . 
FA 6 HOH B 4 1104 19 HOH HOH . 
FA 6 HOH B 5 1105 1 HOH HOH . 
FA 6 HOH B 6 1106 24 HOH HOH . 
FA 6 HOH B 7 1107 8 HOH HOH . 
FA 6 HOH B 8 1108 22 HOH HOH . 
FA 6 HOH B 9 1109 51 HOH HOH . 
FA 6 HOH B 10 1110 50 HOH HOH . 
FA 6 HOH B 11 1111 29 HOH HOH . 
FA 6 HOH B 12 1112 26 HOH HOH . 
FA 6 HOH B 13 1113 23 HOH HOH . 
FA 6 HOH B 14 1114 30 HOH HOH . 
FA 6 HOH B 15 1115 25 HOH HOH . 
FA 6 HOH B 16 1116 21 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 . . . P 3 -31.57 -30.194 17.823 0.97 63.78 ? N SAH 1014 A 1 
HETATM 2 C CA SAH . . . P 3 -32.569 -30.195 18.894 0.97 62.78 ? CA SAH 1014 A 1 
HETATM 3 C CB SAH . . . P 3 -33.808 -30.91 18.331 0.97 44.55 ? CB SAH 1014 A 1 
HETATM 4 C CG SAH . . . P 3 -34.718 -29.936 17.592 0.97 55.17 ? CG SAH 1014 A 1 
HETATM 5 S SD SAH . . . P 3 -35.782 -30.876 16.497 0.97 74.04 ? SD SAH 1014 A 1 
HETATM 6 C C SAH . . . P 3 -32.017 -30.634 20.292 0.97 65.86 ? C SAH 1014 A 1 
HETATM 7 O O SAH . . . P 3 -32.738 -30.643 21.303 0.97 62.94 ? O SAH 1014 A 1 
HETATM 8 O OXT SAH . . . P 3 -30.828 -30.953 20.473 0.97 58.22 ? OXT SAH 1014 A 1 
HETATM 9 C C5' SAH . . . P 3 -36.52 -29.454 15.669 0.97 56 ? C5' SAH 1014 A 1 
HETATM 10 C C4' SAH . . . P 3 -37.992 -29.685 15.95 0.97 64.65 ? C4' SAH 1014 A 1 
HETATM 11 O O4' SAH . . . P 3 -38.808 -28.615 15.535 0.97 70.06 ? O4' SAH 1014 A 1 
HETATM 12 C C3' SAH . . . P 3 -38.551 -30.962 15.328 0.97 56.59 ? C3' SAH 1014 A 1 
HETATM 13 O O3' SAH . . . P 3 -38.87 -31.836 16.375 0.97 76.55 ? O3' SAH 1014 A 1 
HETATM 14 C C2' SAH . . . P 3 -39.908 -30.603 14.783 0.97 59.77 ? C2' SAH 1014 A 1 
HETATM 15 O O2' SAH . . . P 3 -40.903 -31.205 15.591 0.97 61.33 ? O2' SAH 1014 A 1 
HETATM 16 C C1' SAH . . . P 3 -40.007 -29.113 14.985 0.97 63.84 ? C1' SAH 1014 A 1 
HETATM 17 N N9 SAH . . . P 3 -40.111 -28.502 13.664 0.97 64.67 ? N9 SAH 1014 A 1 
HETATM 18 C C8 SAH . . . P 3 -39.165 -28.6 12.683 0.97 71.13 ? C8 SAH 1014 A 1 
HETATM 19 N N7 SAH . . . P 3 -39.63 -27.921 11.605 0.97 66.82 ? N7 SAH 1014 A 1 
HETATM 20 C C5 SAH . . . P 3 -40.826 -27.405 11.932 0.97 56.76 ? C5 SAH 1014 A 1 
HETATM 21 C C6 SAH . . . P 3 -41.694 -26.636 11.211 0.97 58.46 ? C6 SAH 1014 A 1 
HETATM 22 N N6 SAH . . . P 3 -41.294 -26.33 9.976 0.97 71.23 ? N6 SAH 1014 A 1 
HETATM 23 N N1 SAH . . . P 3 -42.89 -26.229 11.741 0.97 49.64 ? N1 SAH 1014 A 1 
HETATM 24 C C2 SAH . . . P 3 -43.227 -26.595 13.014 0.97 62.8 ? C2 SAH 1014 A 1 
HETATM 25 N N3 SAH . . . P 3 -42.344 -27.364 13.744 0.97 73.98 ? N3 SAH 1014 A 1 
HETATM 26 C C4 SAH . . . P 3 -41.16 -27.758 13.215 0.97 62.24 ? C4 SAH 1014 A 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    24 
_model_server_stats.query_time_ms           233 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           26 
#