data_3GEI
#
_model_server_result.job_id            jJUIJDyPobye6ufxeFiJfg 
_model_server_result.datetime_utc      '2024-11-05 00:27:23' 
_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          3gei 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":474}' 
#
_entry.id    3GEI 
#
_exptl.entry_id    3GEI 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              521.208 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER' 
_entity.pdbx_number_of_molecules    2 
_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            3GEI 
_cell.length_a            139.882 
_cell.length_b            224.572 
_cell.length_c            156.788 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3GEI 
_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
PISA dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 author_and_software_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,D,E 1 1,2 
B,C,F 2 1 
#
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' 3_554 -x,y,-z-1/2 -1 0 0 0 1 0 0 0 -1 0 0 -78.394 
#
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 F 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 OG SER 247 A SER 244 1_555 E MG MG . A MG 475 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? 
metalc ? metalc2 D O1G GCP . A GCP 474 1_555 E MG MG . A MG 475 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.162 ? 
metalc ? metalc3 D O2B GCP . A GCP 474 1_555 E MG MG . A MG 475 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? 
#
_chem_comp.formula           'C11 H18 N5 O13 P3' 
_chem_comp.formula_weight    521.208 
_chem_comp.id                GCP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER' 
_chem_comp.type              non-polymer 
_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
PG O1G GCP doub 83 n n 
PG O2G GCP sing 84 n n 
PG O3G GCP sing 85 n n 
PG C3B GCP sing 86 n n 
O2G HOG2 GCP sing 87 n n 
O3G HOG3 GCP sing 88 n n 
C3B PB GCP sing 89 n n 
C3B H3B1 GCP sing 90 n n 
C3B H3B2 GCP sing 91 n n 
PB O1B GCP doub 92 n n 
PB O2B GCP sing 93 n n 
PB O3A GCP sing 94 n n 
O2B HOB2 GCP sing 95 n n 
O3A PA GCP sing 96 n n 
PA O1A GCP doub 97 n n 
PA O2A GCP sing 98 n n 
PA O5' GCP sing 99 n n 
O2A HOA2 GCP sing 100 n n 
O5' C5' GCP sing 101 n n 
C5' C4' GCP sing 102 n n 
C5' "H5'2" GCP sing 103 n n 
C5' "H5'1" GCP sing 104 n n 
C4' O4' GCP sing 105 n n 
C4' C3' GCP sing 106 n n 
C4' H4' GCP sing 107 n n 
O4' C1' GCP sing 108 n n 
C3' O3' GCP sing 109 n n 
C3' C2' GCP sing 110 n n 
C3' H3' GCP sing 111 n n 
O3' HO3' GCP sing 112 n n 
C2' O2' GCP sing 113 n n 
C2' C1' GCP sing 114 n n 
C2' H2' GCP sing 115 n n 
O2' HO2' GCP sing 116 n n 
C1' N9 GCP sing 117 n n 
C1' H1' GCP sing 118 n n 
N9 C8 GCP sing 119 n y 
N9 C4 GCP sing 120 n y 
C8 N7 GCP doub 121 n y 
C8 H8 GCP sing 122 n n 
N7 C5 GCP sing 123 n y 
C5 C6 GCP sing 124 n y 
C5 C4 GCP doub 125 n y 
C6 O6 GCP doub 126 n n 
C6 N1 GCP sing 127 n y 
N1 C2 GCP sing 128 n y 
N1 HN1 GCP sing 129 n n 
C2 N2 GCP sing 130 n n 
C2 N3 GCP doub 131 n y 
N2 HN21 GCP sing 132 n n 
N2 HN22 GCP sing 133 n n 
N3 C4 GCP sing 134 n y 
#
_atom_sites.entry_id                     3GEI 
_atom_sites.fract_transf_matrix[1][1]    0.007149 
_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]    0.004453 
_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]    0.006378 
_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 GCP A 1 474 474 GCP GCP . 
E 3 MG A 1 475 475 MG MG . 
F 2 GCP B 1 474 474 GCP GCP . 
#
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 P PG GCP . . . D 2 -2.596 11.324 -26.358 1 164.08 ? PG GCP 474 A 1 
HETATM 2 O O1G GCP . . . D 2 -2.764 9.826 -26.279 1 163.78 ? O1G GCP 474 A 1 
HETATM 3 O O2G GCP . . . D 2 -2.421 11.985 -25.012 1 164.27 ? O2G GCP 474 A 1 
HETATM 4 O O3G GCP . . . D 2 -3.603 12.01 -27.245 1 164.39 ? O3G GCP 474 A 1 
HETATM 5 C C3B GCP . . . D 2 -1.037 11.615 -27.223 1 163.88 ? C3B GCP 474 A 1 
HETATM 6 P PB GCP . . . D 2 0.2 10.509 -26.513 1 163.89 ? PB GCP 474 A 1 
HETATM 7 O O1B GCP . . . D 2 0.402 10.898 -25.071 1 163.79 ? O1B GCP 474 A 1 
HETATM 8 O O2B GCP . . . D 2 -0.207 9.089 -26.813 1 164.17 ? O2B GCP 474 A 1 
HETATM 9 O O3A GCP . . . D 2 1.599 10.777 -27.263 1 164.3 ? O3A GCP 474 A 1 
HETATM 10 P PA GCP . . . D 2 1.876 10.334 -28.79 1 164.43 ? PA GCP 474 A 1 
HETATM 11 O O1A GCP . . . D 2 3.074 9.414 -28.79 1 164.19 ? O1A GCP 474 A 1 
HETATM 12 O O2A GCP . . . D 2 0.577 9.884 -29.418 1 164.26 ? O2A GCP 474 A 1 
HETATM 13 O O5' GCP . . . D 2 2.315 11.713 -29.503 1 164.72 ? O5' GCP 474 A 1 
HETATM 14 C C5' GCP . . . D 2 3.237 12.6 -28.866 1 165.08 ? C5' GCP 474 A 1 
HETATM 15 C C4' GCP . . . D 2 3.882 13.576 -29.848 1 165.09 ? C4' GCP 474 A 1 
HETATM 16 O O4' GCP . . . D 2 5.084 14.103 -29.268 1 164.97 ? O4' GCP 474 A 1 
HETATM 17 C C3' GCP . . . D 2 4.271 12.916 -31.163 1 165.13 ? C3' GCP 474 A 1 
HETATM 18 O O3' GCP . . . D 2 3.417 13.383 -32.213 1 165.24 ? O3' GCP 474 A 1 
HETATM 19 C C2' GCP . . . D 2 5.728 13.287 -31.396 1 165 ? C2' GCP 474 A 1 
HETATM 20 O O2' GCP . . . D 2 5.855 14.337 -32.362 1 165.22 ? O2' GCP 474 A 1 
HETATM 21 C C1' GCP . . . D 2 6.236 13.787 -30.055 1 164.39 ? C1' GCP 474 A 1 
HETATM 22 N N9 GCP . . . D 2 7.045 12.735 -29.385 1 164.04 ? N9 GCP 474 A 1 
HETATM 23 C C8 GCP . . . D 2 6.595 11.561 -28.897 1 163.95 ? C8 GCP 474 A 1 
HETATM 24 N N7 GCP . . . D 2 7.598 10.836 -28.346 1 163.9 ? N7 GCP 474 A 1 
HETATM 25 C C5 GCP . . . D 2 8.728 11.551 -28.475 1 163.99 ? C5 GCP 474 A 1 
HETATM 26 C C6 GCP . . . D 2 10.158 11.375 -28.109 1 164.11 ? C6 GCP 474 A 1 
HETATM 27 O O6 GCP . . . D 2 10.557 10.348 -27.528 1 164.09 ? O6 GCP 474 A 1 
HETATM 28 N N1 GCP . . . D 2 11.02 12.353 -28.419 1 164.13 ? N1 GCP 474 A 1 
HETATM 29 C C2 GCP . . . D 2 10.626 13.48 -29.048 1 164.18 ? C2 GCP 474 A 1 
HETATM 30 N N2 GCP . . . D 2 11.564 14.419 -29.325 1 164.15 ? N2 GCP 474 A 1 
HETATM 31 N N3 GCP . . . D 2 9.332 13.71 -29.415 1 164.12 ? N3 GCP 474 A 1 
HETATM 32 C C4 GCP . . . D 2 8.357 12.801 -29.16 1 163.98 ? C4 GCP 474 A 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    11 
_model_server_stats.query_time_ms           269 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           32 
#