data_2F3M
#
_model_server_result.job_id            PK7YX5iEHRYnmuhuyNmSKA 
_model_server_result.datetime_utc      '2024-11-28 12:25:13' 
_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          2f3m 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"K","auth_seq_id":5218}' 
#
_entry.id    2F3M 
#
_exptl.entry_id    2F3M 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              520.428 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            1-(S-GLUTATHIONYL)-2,4,6-TRINITROCYCLOHEXA-2,5-DIENE 
_entity.pdbx_number_of_molecules    6 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         120.53 
_cell.angle_beta          106.19 
_cell.angle_gamma         89.97 
_cell.entry_id            2F3M 
_cell.length_a            51.965 
_cell.length_b            93.096 
_cell.length_c            92.998 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2F3M 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 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 dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 author_and_software_defined_assembly 2 
PISA dimeric 2 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,B,G,H,M,N 1 1 
C,D,I,J,O,P 2 1 
E,F,K,L,Q,R 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
? 2 G N N 
? 2 H N N 
? 2 I N N 
? 2 J N N 
? 2 K N N 
? 2 L 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 78 A CYS 77 1_555 A SG CYS 87 A CYS 86 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.879 ? 
disulf ? disulf2 B SG CYS 78 B CYS 77 1_555 B SG CYS 87 B CYS 86 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.943 ? 
disulf ? disulf3 C SG CYS 78 C CYS 77 1_555 C SG CYS 87 C CYS 86 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.199 ? 
disulf ? disulf4 D SG CYS 78 D CYS 77 1_555 D SG CYS 87 D CYS 86 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? 
disulf ? disulf5 E SG CYS 78 E CYS 77 1_555 E SG CYS 87 E CYS 86 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.955 ? 
disulf ? disulf6 F SG CYS 78 F CYS 77 1_555 F SG CYS 87 F CYS 86 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.826 ? 
#
_chem_comp.formula           'C16 H20 N6 O12 S' 
_chem_comp.formula_weight    520.428 
_chem_comp.id                GTD 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              1-(S-GLUTATHIONYL)-2,4,6-TRINITROCYCLOHEXA-2,5-DIENE 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     '(S)-2-AMINO-5-((R)-1-(CARBOXYMETHYLAMINO)-1-OXO-3-(2,4,6-TRINITROCYCLOHEXA-2,5-DIENYLTHIO)PROPAN-2-YLAMINO)-5-OXOPENTANOIC ACID' 
#
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
N1 CA1 GTD sing 129 n n 
N1 HN11 GTD sing 130 n n 
N1 HN12 GTD sing 131 n n 
CA1 C1 GTD sing 132 n n 
CA1 CB1 GTD sing 133 n n 
CA1 HA1 GTD sing 134 n n 
C1 O11 GTD doub 135 n n 
C1 O12 GTD sing 136 n n 
O12 HO1 GTD sing 137 n n 
CB1 CG1 GTD sing 138 n n 
CB1 HB11 GTD sing 139 n n 
CB1 HB12 GTD sing 140 n n 
CG1 CD1 GTD sing 141 n n 
CG1 HG11 GTD sing 142 n n 
CG1 HG12 GTD sing 143 n n 
CD1 OE1 GTD doub 144 n n 
CD1 N2 GTD sing 145 n n 
N2 CA2 GTD sing 146 n n 
N2 HN2 GTD sing 147 n n 
CA2 C2 GTD sing 148 n n 
CA2 CB2 GTD sing 149 n n 
CA2 HA2 GTD sing 150 n n 
C2 O2 GTD doub 151 n n 
C2 N3 GTD sing 152 n n 
CB2 SG2 GTD sing 153 n n 
CB2 HB21 GTD sing 154 n n 
CB2 HB22 GTD sing 155 n n 
SG2 C1' GTD sing 156 n n 
N3 CA3 GTD sing 157 n n 
N3 HN3 GTD sing 158 n n 
CA3 C3 GTD sing 159 n n 
CA3 HA31 GTD sing 160 n n 
CA3 HA32 GTD sing 161 n n 
C3 O31 GTD doub 162 n n 
C3 O32 GTD sing 163 n n 
O32 HO3 GTD sing 164 n n 
C1' C2' GTD sing 165 n n 
C1' C6' GTD sing 166 n n 
C1' H1' GTD sing 167 n n 
C2' N2' GTD sing 168 n n 
C2' C3' GTD doub 169 n n 
N2' O21 GTD doub 170 n n 
N2' O22 GTD sing 171 n n 
C3' C4' GTD sing 172 n n 
C3' H3' GTD sing 173 n n 
C4' N4' GTD sing 174 n n 
C4' C5' GTD sing 175 n n 
C4' H4' GTD sing 176 n n 
N4' O41 GTD doub 177 n n 
N4' O42 GTD sing 178 n n 
C5' C6' GTD doub 179 n n 
C5' H5' GTD sing 180 n n 
C6' N6' GTD sing 181 n n 
N6' O61 GTD doub 182 n n 
N6' O62 GTD sing 183 n n 
#
_atom_sites.entry_id                     2F3M 
_atom_sites.fract_transf_matrix[1][1]    0.019244 
_atom_sites.fract_transf_matrix[1][2]    -0.000009 
_atom_sites.fract_transf_matrix[1][3]    0.006579 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.010742 
_atom_sites.fract_transf_matrix[2][3]    0.006693 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    0.013193 
_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 GTD A 1 1218 218 GTD GTD . 
H 2 GTD B 1 2218 218 GTD GTD . 
I 2 GTD C 1 3218 218 GTD GTD . 
J 2 GTD D 1 4218 218 GTD GTD . 
K 2 GTD E 1 5218 218 GTD GTD . 
L 2 GTD F 1 6218 218 GTD GTD . 
M 3 HOH A 1 1219 4 HOH HOH . 
M 3 HOH A 2 1220 5 HOH HOH . 
M 3 HOH A 3 1221 6 HOH HOH . 
M 3 HOH A 4 1222 7 HOH HOH . 
M 3 HOH A 5 1223 16 HOH HOH . 
M 3 HOH A 6 1224 17 HOH HOH . 
M 3 HOH A 7 1225 21 HOH HOH . 
M 3 HOH A 8 1226 22 HOH HOH . 
M 3 HOH A 9 1227 23 HOH HOH . 
M 3 HOH A 10 1228 28 HOH HOH . 
M 3 HOH A 11 1229 37 HOH HOH . 
M 3 HOH A 12 1230 38 HOH HOH . 
M 3 HOH A 13 1231 50 HOH HOH . 
N 3 HOH B 1 2219 8 HOH HOH . 
N 3 HOH B 2 2220 9 HOH HOH . 
N 3 HOH B 3 2221 10 HOH HOH . 
N 3 HOH B 4 2222 15 HOH HOH . 
N 3 HOH B 5 2223 19 HOH HOH . 
N 3 HOH B 6 2224 20 HOH HOH . 
N 3 HOH B 7 2225 44 HOH HOH . 
N 3 HOH B 8 2226 51 HOH HOH . 
O 3 HOH C 1 3219 11 HOH HOH . 
O 3 HOH C 2 3220 12 HOH HOH . 
O 3 HOH C 3 3221 29 HOH HOH . 
O 3 HOH C 4 3222 42 HOH HOH . 
O 3 HOH C 5 3223 45 HOH HOH . 
O 3 HOH C 6 3224 52 HOH HOH . 
O 3 HOH C 7 3225 53 HOH HOH . 
O 3 HOH C 8 3226 54 HOH HOH . 
P 3 HOH D 1 4219 13 HOH HOH . 
P 3 HOH D 2 4220 14 HOH HOH . 
P 3 HOH D 3 4221 30 HOH HOH . 
P 3 HOH D 4 4222 31 HOH HOH . 
P 3 HOH D 5 4223 32 HOH HOH . 
P 3 HOH D 6 4224 33 HOH HOH . 
P 3 HOH D 7 4225 34 HOH HOH . 
P 3 HOH D 8 4226 35 HOH HOH . 
P 3 HOH D 9 4227 36 HOH HOH . 
P 3 HOH D 10 4228 55 HOH HOH . 
Q 3 HOH E 1 5219 3 HOH HOH . 
Q 3 HOH E 2 5220 26 HOH HOH . 
Q 3 HOH E 3 5221 41 HOH HOH . 
Q 3 HOH E 4 5222 46 HOH HOH . 
Q 3 HOH E 5 5223 47 HOH HOH . 
Q 3 HOH E 6 5224 49 HOH HOH . 
R 3 HOH F 1 6219 2 HOH HOH . 
R 3 HOH F 2 6220 24 HOH HOH . 
R 3 HOH F 3 6221 25 HOH HOH . 
R 3 HOH F 4 6222 27 HOH HOH . 
R 3 HOH F 5 6223 39 HOH HOH . 
R 3 HOH F 6 6224 40 HOH HOH . 
R 3 HOH F 7 6225 43 HOH HOH . 
R 3 HOH F 8 6226 48 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 N1 GTD . . . K 2 -57.627 -91.708 48.538 1 52.11 ? N1 GTD 5218 E 1 
HETATM 2 C CA1 GTD . . . K 2 -58.586 -90.743 48.067 1 52.18 ? CA1 GTD 5218 E 1 
HETATM 3 C C1 GTD . . . K 2 -58.004 -90.019 46.911 1 52.2 ? C1 GTD 5218 E 1 
HETATM 4 O O11 GTD . . . K 2 -58.738 -89.747 45.948 1 51.95 ? O11 GTD 5218 E 1 
HETATM 5 O O12 GTD . . . K 2 -56.802 -89.721 46.96 1 51.91 ? O12 GTD 5218 E 1 
HETATM 6 C CB1 GTD . . . K 2 -58.85 -89.764 49.183 1 52.45 ? CB1 GTD 5218 E 1 
HETATM 7 C CG1 GTD . . . K 2 -60.238 -89.186 49.048 1 53.11 ? CG1 GTD 5218 E 1 
HETATM 8 C CD1 GTD . . . K 2 -60.498 -88.299 50.226 1 53.4 ? CD1 GTD 5218 E 1 
HETATM 9 O OE1 GTD . . . K 2 -59.995 -88.542 51.301 1 53.4 ? OE1 GTD 5218 E 1 
HETATM 10 N N2 GTD . . . K 2 -61.294 -87.274 49.994 1 53.86 ? N2 GTD 5218 E 1 
HETATM 11 C CA2 GTD . . . K 2 -61.762 -86.435 51.06 1 54.37 ? CA2 GTD 5218 E 1 
HETATM 12 C C2 GTD . . . K 2 -63.246 -86.287 50.988 1 54.1 ? C2 GTD 5218 E 1 
HETATM 13 O O2 GTD . . . K 2 -63.764 -85.222 51.193 1 54.15 ? O2 GTD 5218 E 1 
HETATM 14 C CB2 GTD . . . K 2 -61.035 -85.102 50.982 1 54.84 ? CB2 GTD 5218 E 1 
HETATM 15 S SG2 GTD . . . K 2 -59.296 -85.303 51.126 1 56.08 ? SG2 GTD 5218 E 1 
HETATM 16 N N3 GTD . . . K 2 -63.944 -87.367 50.691 1 53.99 ? N3 GTD 5218 E 1 
HETATM 17 C CA3 GTD . . . K 2 -65.378 -87.317 50.539 1 53.92 ? CA3 GTD 5218 E 1 
HETATM 18 C C3 GTD . . . K 2 -66.077 -88.476 51.199 1 53.98 ? C3 GTD 5218 E 1 
HETATM 19 O O31 GTD . . . K 2 -65.4 -89.283 51.857 1 54.08 ? O31 GTD 5218 E 1 
HETATM 20 O O32 GTD . . . K 2 -67.309 -88.599 51.07 1 54.05 ? O32 GTD 5218 E 1 
HETATM 21 C C1' GTD . . . K 2 -58.873 -84.425 52.598 0.7 56.53 ? C1' GTD 5218 E 1 
HETATM 22 C C2' GTD . . . K 2 -57.485 -83.846 52.498 0.7 56.91 ? C2' GTD 5218 E 1 
HETATM 23 N N2' GTD . . . K 2 -57.266 -82.551 51.901 0.7 56.92 ? N2' GTD 5218 E 1 
HETATM 24 O O21 GTD . . . K 2 -58.127 -81.816 51.811 0.7 56.99 ? O21 GTD 5218 E 1 
HETATM 25 O O22 GTD . . . K 2 -56.182 -82.256 51.424 0.7 57.07 ? O22 GTD 5218 E 1 
HETATM 26 C C3' GTD . . . K 2 -56.426 -84.48 53.002 0.7 56.87 ? C3' GTD 5218 E 1 
HETATM 27 C C4' GTD . . . K 2 -56.591 -85.011 54.397 0.7 57.14 ? C4' GTD 5218 E 1 
HETATM 28 N N4' GTD . . . K 2 -55.522 -85.659 54.833 0.7 57.11 ? N4' GTD 5218 E 1 
HETATM 29 O O41 GTD . . . K 2 -54.627 -85.94 54.058 0.7 57.33 ? O41 GTD 5218 E 1 
HETATM 30 O O42 GTD . . . K 2 -55.44 -85.959 56.01 0.7 57.28 ? O42 GTD 5218 E 1 
HETATM 31 C C5' GTD . . . K 2 -57.843 -85.845 54.355 0.7 56.84 ? C5' GTD 5218 E 1 
HETATM 32 C C6' GTD . . . K 2 -58.94 -85.275 53.842 0.7 56.91 ? C6' GTD 5218 E 1 
HETATM 33 N N6' GTD . . . K 2 -60.187 -85.445 54.564 0.7 56.92 ? N6' GTD 5218 E 1 
HETATM 34 O O61 GTD . . . K 2 -60.451 -84.699 55.491 0.7 57.06 ? O61 GTD 5218 E 1 
HETATM 35 O O62 GTD . . . K 2 -60.959 -86.335 54.263 0.7 57.15 ? O62 GTD 5218 E 1 
#
_model_server_stats.io_time_ms              62 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    10 
_model_server_stats.query_time_ms           297 
_model_server_stats.encode_time_ms          10 
_model_server_stats.element_count           35 
#