data_3D67
#
_model_server_result.job_id            ksFzO3EkLHqVKlMu4aIU-A 
_model_server_result.datetime_utc      '2024-11-02 20:27:50' 
_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          3d67 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"O","auth_seq_id":660}' 
#
_entry.id    3D67 
#
_exptl.entry_id    3D67 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              235.261 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '(2-GUANIDINOETHYLMERCAPTO)SUCCINIC ACID' 
_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            3D67 
_cell.length_a            161.05 
_cell.length_b            161.05 
_cell.length_c            138.99 
_cell.Z_PDB               18 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3D67 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        152 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 31 2 1' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA monomeric 1 author_and_software_defined_assembly 1 
PISA monomeric 1 author_and_software_defined_assembly 2 
PISA monomeric 1 author_and_software_defined_assembly 3 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,D,E,F,G,H,I 1 1 
B,J,K,L,M,N,O 2 1 
C,P,Q,R,S,T 3 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 I N N 
? 4 O N N 
? 4 T 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 179 A CYS 156 1_555 A SG CYS 192 A CYS 169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf2 A SG CYS 251 A CYS 228 1_555 A SG CYS 275 A CYS 252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? 
disulf ? disulf3 A SG CYS 266 A CYS 243 1_555 A SG CYS 280 A CYS 257 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.084 ? 
disulf ? disulf4 B SG CYS 179 B CYS 156 1_555 B SG CYS 192 B CYS 169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? 
disulf ? disulf5 B SG CYS 251 B CYS 228 1_555 B SG CYS 275 B CYS 252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? 
disulf ? disulf6 B SG CYS 266 B CYS 243 1_555 B SG CYS 280 B CYS 257 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.111 ? 
disulf ? disulf7 C SG CYS 179 C CYS 156 1_555 C SG CYS 192 C CYS 169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? 
disulf ? disulf8 C SG CYS 251 C CYS 228 1_555 C SG CYS 275 C CYS 252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? 
disulf ? disulf9 C SG CYS 266 C CYS 243 1_555 C SG CYS 280 C CYS 257 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.122 ? 
covale ? covale1 A ND2 ASN 45 A ASN 22 1_555 D C1 NAG . A NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? 
covale ? covale2 A ND2 ASN 74 A ASN 51 1_555 E C1 NAG . A NAG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.464 ? 
covale ? covale3 A ND2 ASN 86 A ASN 63 1_555 F C1 NAG . A NAG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.476 ? 
covale ? covale4 A ND2 ASN 109 A ASN 86 1_555 G C1 NAG . A NAG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.461 ? 
covale ? covale5 B ND2 ASN 45 B ASN 22 1_555 J C1 NAG . B NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? 
covale ? covale6 B ND2 ASN 74 B ASN 51 1_555 K C1 NAG . B NAG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.459 ? 
covale ? covale7 B ND2 ASN 86 B ASN 63 1_555 L C1 NAG . B NAG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.461 ? 
covale ? covale8 B ND2 ASN 109 B ASN 86 1_555 M C1 NAG . B NAG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? 
covale ? covale9 C ND2 ASN 45 C ASN 22 1_555 P C1 NAG . C NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.461 ? 
covale ? covale10 C ND2 ASN 74 C ASN 51 1_555 Q C1 NAG . C NAG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? 
covale ? covale11 C ND2 ASN 109 C ASN 86 1_555 R C1 NAG . C NAG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? 
metalc ? metalc1 A ND1 HIS 182 A HIS 159 1_555 H ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.085 ? 
metalc ? metalc2 A OE1 GLU 185 A GLU 162 1_555 H ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.013 ? 
metalc ? metalc3 A OE2 GLU 185 A GLU 162 1_555 H ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? 
metalc ? metalc4 A ND1 HIS 311 A HIS 288 1_555 H ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? 
metalc ? metalc5 H ZN ZN . A ZN 501 1_555 I O13 GEM . A GEM 660 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.667 ? 
metalc ? metalc6 B ND1 HIS 182 B HIS 159 1_555 N ZN ZN . B ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? 
metalc ? metalc7 B OE1 GLU 185 B GLU 162 1_555 N ZN ZN . B ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.011 ? 
metalc ? metalc8 B OE2 GLU 185 B GLU 162 1_555 N ZN ZN . B ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? 
metalc ? metalc9 B ND1 HIS 311 B HIS 288 1_555 N ZN ZN . B ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.093 ? 
metalc ? metalc10 N ZN ZN . B ZN 501 1_555 O O13 GEM . B GEM 660 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? 
metalc ? metalc11 C ND1 HIS 182 C HIS 159 1_555 S ZN ZN . C ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? 
metalc ? metalc12 C OE1 GLU 185 C GLU 162 1_555 S ZN ZN . C ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
metalc ? metalc13 C OE2 GLU 185 C GLU 162 1_555 S ZN ZN . C ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.997 ? 
metalc ? metalc14 C ND1 HIS 311 C HIS 288 1_555 S ZN ZN . C ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? 
metalc ? metalc15 S ZN ZN . C ZN 501 1_555 T O13 GEM . C GEM 660 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.143 ? 
#
_chem_comp.formula           'C7 H13 N3 O4 S' 
_chem_comp.formula_weight    235.261 
_chem_comp.id                GEM 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '(2-GUANIDINOETHYLMERCAPTO)SUCCINIC ACID' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     '2-GUANIDINOETHYLTHIO)SUCCINIC ACID;GUANIDINOETHYL MERCAPTOSUCCINIC ACID;GEMSA' 
#
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
C8 S7 GEM sing 83 n n 
C8 C9 GEM sing 84 n n 
C8 C10 GEM sing 85 n n 
C8 HC8 GEM sing 86 n n 
S7 C6 GEM sing 87 n n 
C6 C5 GEM sing 88 n n 
C6 HC61 GEM sing 89 n n 
C6 HC62 GEM sing 90 n n 
C5 N3 GEM sing 91 n n 
C5 HC51 GEM sing 92 n n 
C5 HC52 GEM sing 93 n n 
N3 C1 GEM sing 94 n n 
N3 HN3 GEM sing 95 n n 
C1 N4 GEM sing 96 n n 
C1 N2 GEM doub 97 n n 
N4 HN41 GEM sing 98 n n 
N4 HN42 GEM sing 99 n n 
N2 HN21 GEM sing 100 n n 
C9 O14 GEM sing 101 n n 
C9 O15 GEM doub 102 n n 
O14 HO41 GEM sing 103 n n 
C10 C11 GEM sing 104 n n 
C10 H101 GEM sing 105 n n 
C10 H102 GEM sing 106 n n 
C11 O12 GEM doub 107 n n 
C11 O13 GEM sing 108 n n 
O13 HO31 GEM sing 109 n n 
#
_atom_sites.entry_id                     3D67 
_atom_sites.fract_transf_matrix[1][1]    0.006209 
_atom_sites.fract_transf_matrix[1][2]    0.003585 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.00717 
_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]    0.007195 
_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
D 2 NAG A 1 601 601 NAG NAG . 
E 2 NAG A 1 602 602 NAG NAG . 
F 2 NAG A 1 603 603 NAG NAG . 
G 2 NAG A 1 604 604 NAG NAG . 
H 3 ZN A 1 501 501 ZN ZN . 
I 4 GEM A 1 660 660 GEM GEM . 
J 2 NAG B 1 601 601 NAG NAG . 
K 2 NAG B 1 602 602 NAG NAG . 
L 2 NAG B 1 603 603 NAG NAG . 
M 2 NAG B 1 604 604 NAG NAG . 
N 3 ZN B 1 501 501 ZN ZN . 
O 4 GEM B 1 660 660 GEM GEM . 
P 2 NAG C 1 601 601 NAG NAG . 
Q 2 NAG C 1 602 602 NAG NAG . 
R 2 NAG C 1 604 604 NAG NAG . 
S 3 ZN C 1 501 501 ZN ZN . 
T 4 GEM C 1 660 660 GEM GEM . 
#
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 C8 GEM . . . O 4 58.286 -2.547 20.61 1 124.14 ? C8 GEM 660 B 1 
HETATM 2 S S7 GEM . . . O 4 56.742 -2.333 21.597 1 125.06 ? S7 GEM 660 B 1 
HETATM 3 C C6 GEM . . . O 4 56.74 -0.574 22.004 1 125.69 ? C6 GEM 660 B 1 
HETATM 4 C C5 GEM . . . O 4 57.089 0.328 20.814 1 126.23 ? C5 GEM 660 B 1 
HETATM 5 N N3 GEM . . . O 4 57.403 1.683 21.232 1 126.68 ? N3 GEM 660 B 1 
HETATM 6 C C1 GEM . . . O 4 56.519 2.494 21.79 1 126.73 ? C1 GEM 660 B 1 
HETATM 7 N N4 GEM . . . O 4 55.912 3.406 21.048 1 126.88 ? N4 GEM 660 B 1 
HETATM 8 N N2 GEM . . . O 4 56.269 2.399 23.089 1 126.51 ? N2 GEM 660 B 1 
HETATM 9 C C9 GEM . . . O 4 58.25 -2.137 19.139 1 122.7 ? C9 GEM 660 B 1 
HETATM 10 O O14 GEM . . . O 4 57.188 -2.195 18.494 1 121.4 ? O14 GEM 660 B 1 
HETATM 11 O O15 GEM . . . O 4 59.312 -1.77 18.611 1 121.19 ? O15 GEM 660 B 1 
HETATM 12 C C10 GEM . . . O 4 58.695 -4.022 20.628 1 124.21 ? C10 GEM 660 B 1 
HETATM 13 C C11 GEM . . . O 4 57.482 -4.902 20.463 1 123.56 ? C11 GEM 660 B 1 
HETATM 14 O O12 GEM . . . O 4 56.961 -5.391 21.481 1 122.82 ? O12 GEM 660 B 1 
HETATM 15 O O13 GEM . . . O 4 57.034 -5.091 19.317 1 123.31 ? O13 GEM 660 B 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    10 
_model_server_stats.query_time_ms           267 
_model_server_stats.encode_time_ms          12 
_model_server_stats.element_count           15 
#