data_2P5M
#
_model_server_result.job_id            S7fLg64TYDQzywtfmvkHXw 
_model_server_result.datetime_utc      '2025-01-02 17:54:01' 
_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          2p5m 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":202}' 
#
_entry.id    2P5M 
#
_exptl.entry_id    2P5M 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              175.209 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            ARGININE 
_entity.pdbx_number_of_molecules    5 
_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            2P5M 
_cell.length_a            117.014 
_cell.length_b            117.014 
_cell.length_c            68.927 
_cell.Z_PDB               36 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2P5M 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        179 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 65 2 2' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    hexameric 
_pdbx_struct_assembly.oligomeric_count      6 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G,H,I,J,K 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 11_555 -x+y,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 0 0 34.4635 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 D N N 
? 2 E N N 
? 2 F N N 
? 2 G N N 
? 2 H N N 
#
_chem_comp.formula           'C6 H15 N4 O2 1' 
_chem_comp.formula_weight    175.209 
_chem_comp.id                ARG 
_chem_comp.mon_nstd_flag     y 
_chem_comp.name              ARGININE 
_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 ARG sing 13 n n 
N H ARG sing 14 n n 
N H2 ARG sing 15 n n 
CA C ARG sing 16 n n 
CA CB ARG sing 17 n n 
CA HA ARG sing 18 n n 
C O ARG doub 19 n n 
C OXT ARG sing 20 n n 
CB CG ARG sing 21 n n 
CB HB2 ARG sing 22 n n 
CB HB3 ARG sing 23 n n 
CG CD ARG sing 24 n n 
CG HG2 ARG sing 25 n n 
CG HG3 ARG sing 26 n n 
CD NE ARG sing 27 n n 
CD HD2 ARG sing 28 n n 
CD HD3 ARG sing 29 n n 
NE CZ ARG sing 30 n n 
NE HE ARG sing 31 n n 
CZ NH1 ARG sing 32 n n 
CZ NH2 ARG doub 33 n n 
NH1 HH11 ARG sing 34 n n 
NH1 HH12 ARG sing 35 n n 
NH2 HH21 ARG sing 36 n n 
NH2 HH22 ARG sing 37 n n 
OXT HXT ARG sing 38 n n 
#
_atom_sites.entry_id                     2P5M 
_atom_sites.fract_transf_matrix[1][1]    0.008546 
_atom_sites.fract_transf_matrix[1][2]    0.004934 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.009868 
_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]    0.014508 
_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 ARG B 1 201 201 ARG ARG . 
E 2 ARG B 1 202 202 ARG ARG . 
F 2 ARG B 1 203 203 ARG ARG . 
G 2 ARG B 1 204 204 ARG ARG . 
H 2 ARG B 1 205 205 ARG ARG . 
I 3 HOH A 1 150 2 HOH HOH . 
I 3 HOH A 2 151 5 HOH HOH . 
I 3 HOH A 3 152 9 HOH HOH . 
I 3 HOH A 4 153 13 HOH HOH . 
I 3 HOH A 5 154 15 HOH HOH . 
I 3 HOH A 6 155 17 HOH HOH . 
I 3 HOH A 7 156 18 HOH HOH . 
I 3 HOH A 8 157 19 HOH HOH . 
I 3 HOH A 9 158 21 HOH HOH . 
I 3 HOH A 10 159 23 HOH HOH . 
I 3 HOH A 11 160 29 HOH HOH . 
I 3 HOH A 12 161 32 HOH HOH . 
I 3 HOH A 13 162 37 HOH HOH . 
I 3 HOH A 14 163 39 HOH HOH . 
I 3 HOH A 15 164 41 HOH HOH . 
I 3 HOH A 16 165 47 HOH HOH . 
I 3 HOH A 17 166 48 HOH HOH . 
I 3 HOH A 18 167 53 HOH HOH . 
I 3 HOH A 19 168 59 HOH HOH . 
I 3 HOH A 20 169 60 HOH HOH . 
I 3 HOH A 21 170 66 HOH HOH . 
I 3 HOH A 22 171 67 HOH HOH . 
I 3 HOH A 23 172 68 HOH HOH . 
I 3 HOH A 24 173 69 HOH HOH . 
I 3 HOH A 25 174 73 HOH HOH . 
I 3 HOH A 26 175 76 HOH HOH . 
I 3 HOH A 27 176 80 HOH HOH . 
I 3 HOH A 28 177 81 HOH HOH . 
I 3 HOH A 29 178 82 HOH HOH . 
I 3 HOH A 30 179 83 HOH HOH . 
I 3 HOH A 31 180 84 HOH HOH . 
I 3 HOH A 32 181 86 HOH HOH . 
I 3 HOH A 33 182 88 HOH HOH . 
I 3 HOH A 34 183 90 HOH HOH . 
I 3 HOH A 35 184 91 HOH HOH . 
I 3 HOH A 36 185 94 HOH HOH . 
I 3 HOH A 37 186 98 HOH HOH . 
I 3 HOH A 38 187 104 HOH HOH . 
I 3 HOH A 39 188 105 HOH HOH . 
I 3 HOH A 40 189 108 HOH HOH . 
I 3 HOH A 41 190 110 HOH HOH . 
I 3 HOH A 42 191 112 HOH HOH . 
I 3 HOH A 43 192 114 HOH HOH . 
I 3 HOH A 44 193 115 HOH HOH . 
I 3 HOH A 45 194 123 HOH HOH . 
I 3 HOH A 46 195 125 HOH HOH . 
I 3 HOH A 47 196 135 HOH HOH . 
I 3 HOH A 48 197 140 HOH HOH . 
I 3 HOH A 49 198 143 HOH HOH . 
I 3 HOH A 50 199 146 HOH HOH . 
I 3 HOH A 51 200 147 HOH HOH . 
I 3 HOH A 52 201 152 HOH HOH . 
I 3 HOH A 53 202 153 HOH HOH . 
I 3 HOH A 54 203 154 HOH HOH . 
I 3 HOH A 55 204 155 HOH HOH . 
I 3 HOH A 56 205 156 HOH HOH . 
I 3 HOH A 57 206 157 HOH HOH . 
I 3 HOH A 58 207 158 HOH HOH . 
I 3 HOH A 59 208 159 HOH HOH . 
I 3 HOH A 60 209 164 HOH HOH . 
I 3 HOH A 61 210 167 HOH HOH . 
I 3 HOH A 62 211 168 HOH HOH . 
J 3 HOH B 1 206 1 HOH HOH . 
J 3 HOH B 2 207 3 HOH HOH . 
J 3 HOH B 3 208 4 HOH HOH . 
J 3 HOH B 4 209 7 HOH HOH . 
J 3 HOH B 5 210 11 HOH HOH . 
J 3 HOH B 6 211 14 HOH HOH . 
J 3 HOH B 7 212 16 HOH HOH . 
J 3 HOH B 8 213 22 HOH HOH . 
J 3 HOH B 9 214 25 HOH HOH . 
J 3 HOH B 10 215 27 HOH HOH . 
J 3 HOH B 11 216 28 HOH HOH . 
J 3 HOH B 12 217 30 HOH HOH . 
J 3 HOH B 13 218 31 HOH HOH . 
J 3 HOH B 14 219 34 HOH HOH . 
J 3 HOH B 15 220 36 HOH HOH . 
J 3 HOH B 16 221 38 HOH HOH . 
J 3 HOH B 17 222 43 HOH HOH . 
J 3 HOH B 18 223 44 HOH HOH . 
J 3 HOH B 19 224 46 HOH HOH . 
J 3 HOH B 20 225 49 HOH HOH . 
J 3 HOH B 21 226 54 HOH HOH . 
J 3 HOH B 22 227 61 HOH HOH . 
J 3 HOH B 23 228 62 HOH HOH . 
J 3 HOH B 24 229 63 HOH HOH . 
J 3 HOH B 25 230 65 HOH HOH . 
J 3 HOH B 26 231 70 HOH HOH . 
J 3 HOH B 27 232 74 HOH HOH . 
J 3 HOH B 28 233 75 HOH HOH . 
J 3 HOH B 29 234 77 HOH HOH . 
J 3 HOH B 30 235 78 HOH HOH . 
J 3 HOH B 31 236 79 HOH HOH . 
J 3 HOH B 32 237 87 HOH HOH . 
J 3 HOH B 33 238 89 HOH HOH . 
J 3 HOH B 34 239 92 HOH HOH . 
J 3 HOH B 35 240 93 HOH HOH . 
J 3 HOH B 36 241 96 HOH HOH . 
J 3 HOH B 37 242 97 HOH HOH . 
J 3 HOH B 38 243 100 HOH HOH . 
J 3 HOH B 39 244 106 HOH HOH . 
J 3 HOH B 40 245 107 HOH HOH . 
J 3 HOH B 41 246 119 HOH HOH . 
J 3 HOH B 42 247 120 HOH HOH . 
J 3 HOH B 43 248 121 HOH HOH . 
J 3 HOH B 44 249 122 HOH HOH . 
J 3 HOH B 45 250 124 HOH HOH . 
J 3 HOH B 46 251 126 HOH HOH . 
J 3 HOH B 47 252 128 HOH HOH . 
J 3 HOH B 48 253 133 HOH HOH . 
J 3 HOH B 49 254 134 HOH HOH . 
J 3 HOH B 50 255 136 HOH HOH . 
J 3 HOH B 51 256 137 HOH HOH . 
J 3 HOH B 52 257 142 HOH HOH . 
J 3 HOH B 53 258 145 HOH HOH . 
J 3 HOH B 54 259 149 HOH HOH . 
J 3 HOH B 55 260 150 HOH HOH . 
J 3 HOH B 56 261 161 HOH HOH . 
J 3 HOH B 57 262 162 HOH HOH . 
J 3 HOH B 58 263 163 HOH HOH . 
J 3 HOH B 59 264 165 HOH HOH . 
J 3 HOH B 60 265 166 HOH HOH . 
J 3 HOH B 61 266 169 HOH HOH . 
K 3 HOH C 1 150 6 HOH HOH . 
K 3 HOH C 2 151 8 HOH HOH . 
K 3 HOH C 3 152 10 HOH HOH . 
K 3 HOH C 4 153 12 HOH HOH . 
K 3 HOH C 5 154 20 HOH HOH . 
K 3 HOH C 6 155 24 HOH HOH . 
K 3 HOH C 7 156 26 HOH HOH . 
K 3 HOH C 8 157 33 HOH HOH . 
K 3 HOH C 9 158 35 HOH HOH . 
K 3 HOH C 10 159 40 HOH HOH . 
K 3 HOH C 11 160 42 HOH HOH . 
K 3 HOH C 12 161 45 HOH HOH . 
K 3 HOH C 13 162 50 HOH HOH . 
K 3 HOH C 14 163 51 HOH HOH . 
K 3 HOH C 15 164 52 HOH HOH . 
K 3 HOH C 16 165 55 HOH HOH . 
K 3 HOH C 17 166 56 HOH HOH . 
K 3 HOH C 18 167 57 HOH HOH . 
K 3 HOH C 19 168 58 HOH HOH . 
K 3 HOH C 20 169 64 HOH HOH . 
K 3 HOH C 21 170 71 HOH HOH . 
K 3 HOH C 22 171 72 HOH HOH . 
K 3 HOH C 23 172 85 HOH HOH . 
K 3 HOH C 24 173 95 HOH HOH . 
K 3 HOH C 25 174 99 HOH HOH . 
K 3 HOH C 26 175 101 HOH HOH . 
K 3 HOH C 27 176 102 HOH HOH . 
K 3 HOH C 28 177 103 HOH HOH . 
K 3 HOH C 29 178 109 HOH HOH . 
K 3 HOH C 30 179 111 HOH HOH . 
K 3 HOH C 31 180 113 HOH HOH . 
K 3 HOH C 32 181 116 HOH HOH . 
K 3 HOH C 33 182 117 HOH HOH . 
K 3 HOH C 34 183 118 HOH HOH . 
K 3 HOH C 35 184 127 HOH HOH . 
K 3 HOH C 36 185 129 HOH HOH . 
K 3 HOH C 37 186 130 HOH HOH . 
K 3 HOH C 38 187 131 HOH HOH . 
K 3 HOH C 39 188 132 HOH HOH . 
K 3 HOH C 40 189 138 HOH HOH . 
K 3 HOH C 41 190 139 HOH HOH . 
K 3 HOH C 42 191 141 HOH HOH . 
K 3 HOH C 43 192 144 HOH HOH . 
K 3 HOH C 44 193 148 HOH HOH . 
K 3 HOH C 45 194 151 HOH HOH . 
K 3 HOH C 46 195 160 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 ARG . . . E 2 8.266 97.44 10.371 1 10.51 ? N ARG 202 B 1 
HETATM 2 C CA ARG . . . E 2 7.653 97.564 11.699 1 11.03 ? CA ARG 202 B 1 
HETATM 3 C C ARG . . . E 2 7.046 96.229 12.092 1 11.45 ? C ARG 202 B 1 
HETATM 4 O O ARG . . . E 2 6.778 95.981 13.272 1 10.69 ? O ARG 202 B 1 
HETATM 5 C CB ARG . . . E 2 6.561 98.631 11.675 1 10.85 ? CB ARG 202 B 1 
HETATM 6 C CG ARG . . . E 2 5.385 98.339 10.725 1 10.04 ? CG ARG 202 B 1 
HETATM 7 C CD ARG . . . E 2 4.462 99.549 10.699 1 11.69 ? CD ARG 202 B 1 
HETATM 8 N NE ARG . . . E 2 3.314 99.396 9.815 1 9.13 ? NE ARG 202 B 1 
HETATM 9 C CZ ARG . . . E 2 2.146 98.88 10.175 1 10.25 ? CZ ARG 202 B 1 
HETATM 10 N NH1 ARG . . . E 2 1.963 98.427 11.405 1 10.59 ? NH1 ARG 202 B 1 
HETATM 11 N NH2 ARG . . . E 2 1.153 98.83 9.3 1 9.79 ? NH2 ARG 202 B 1 
HETATM 12 O OXT ARG . . . E 2 6.796 95.414 11.184 1 11.65 ? OXT ARG 202 B 1 
#
_model_server_stats.io_time_ms              6 
_model_server_stats.parse_time_ms           14 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           306 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           12 
#