data_8DPB
#
_model_server_result.job_id            dlctJtUul1bclw1-09S3KQ 
_model_server_result.datetime_utc      '2025-01-11 12:46:22' 
_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          8dpb 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"I","auth_seq_id":401}' 
#
_entry.id    8DPB 
#
_exptl.entry_id    8DPB 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              521.208 
_entity.id                          3 
_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            8DPB 
_cell.length_a            66.23 
_cell.length_b            80.98 
_cell.length_c            166.38 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8DPB 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    'P 2ac 2ab' 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_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,L,M,N 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    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 E N N 
? 3 I 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 69 A SER 69 1_555 F MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.093 ? 
metalc ? metalc2 A OD1 ASP 105 A ASP 105 1_555 F MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.099 ? 
metalc ? metalc3 A OE1 GLU 154 A GLU 154 1_555 F MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.1 ? 
metalc ? metalc4 E O3G GCP . A GCP 401 1_555 F MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.096 ? 
metalc ? metalc5 E O1B GCP . A GCP 401 1_555 F MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.099 ? 
metalc ? metalc6 F MG MG . A MG 402 1_555 K O HOH . A HOH 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.102 ? 
metalc ? metalc7 B OG SER 69 B SER 69 1_555 J MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.095 ? 
metalc ? metalc8 B OD1 ASP 105 B ASP 105 1_555 J MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.1 ? 
metalc ? metalc9 B OE1 GLU 154 B GLU 154 1_555 J MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.099 ? 
metalc ? metalc10 I O3G GCP . B GCP 401 1_555 J MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.091 ? 
metalc ? metalc11 I O1B GCP . B GCP 401 1_555 J MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.101 ? 
metalc ? metalc12 J MG MG . B MG 402 1_555 L O HOH . B HOH 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.099 ? 
#
_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                     8DPB 
_atom_sites.fract_transf_matrix[1][1]    0.015099 
_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]    0.012349 
_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]    0.00601 
_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
E 3 GCP A 1 401 401 GCP GCP . 
F 4 MG A 1 402 402 MG MG . 
G 5 GOL A 1 403 501 GOL GOL . 
H 5 GOL A 1 404 601 GOL GOL . 
I 3 GCP B 1 401 401 GCP GCP . 
J 4 MG B 1 402 402 MG MG . 
K 6 HOH A 1 501 29 HOH HOH . 
K 6 HOH A 2 502 22 HOH HOH . 
K 6 HOH A 3 503 54 HOH HOH . 
K 6 HOH A 4 504 24 HOH HOH . 
K 6 HOH A 5 505 1 HOH HOH . 
K 6 HOH A 6 506 403 HOH HOH . 
K 6 HOH A 7 507 19 HOH HOH . 
K 6 HOH A 8 508 12 HOH HOH . 
K 6 HOH A 9 509 13 HOH HOH . 
K 6 HOH A 10 510 52 HOH HOH . 
K 6 HOH A 11 511 35 HOH HOH . 
K 6 HOH A 12 512 27 HOH HOH . 
K 6 HOH A 13 513 48 HOH HOH . 
K 6 HOH A 14 514 30 HOH HOH . 
K 6 HOH A 15 515 18 HOH HOH . 
K 6 HOH A 16 516 10 HOH HOH . 
K 6 HOH A 17 517 20 HOH HOH . 
K 6 HOH A 18 518 55 HOH HOH . 
K 6 HOH A 19 519 6 HOH HOH . 
K 6 HOH A 20 520 33 HOH HOH . 
K 6 HOH A 21 521 7 HOH HOH . 
K 6 HOH A 22 522 28 HOH HOH . 
K 6 HOH A 23 523 53 HOH HOH . 
K 6 HOH A 24 524 31 HOH HOH . 
K 6 HOH A 25 525 23 HOH HOH . 
L 6 HOH B 1 501 59 HOH HOH . 
L 6 HOH B 2 502 65 HOH HOH . 
L 6 HOH B 3 503 14 HOH HOH . 
L 6 HOH B 4 504 38 HOH HOH . 
L 6 HOH B 5 505 64 HOH HOH . 
L 6 HOH B 6 506 403 HOH HOH . 
L 6 HOH B 7 507 32 HOH HOH . 
L 6 HOH B 8 508 40 HOH HOH . 
L 6 HOH B 9 509 36 HOH HOH . 
L 6 HOH B 10 510 3 HOH HOH . 
L 6 HOH B 11 511 15 HOH HOH . 
L 6 HOH B 12 512 57 HOH HOH . 
L 6 HOH B 13 513 8 HOH HOH . 
L 6 HOH B 14 514 50 HOH HOH . 
L 6 HOH B 15 515 2 HOH HOH . 
L 6 HOH B 16 516 62 HOH HOH . 
L 6 HOH B 17 517 4 HOH HOH . 
L 6 HOH B 18 518 41 HOH HOH . 
L 6 HOH B 19 519 58 HOH HOH . 
L 6 HOH B 20 520 37 HOH HOH . 
L 6 HOH B 21 521 34 HOH HOH . 
L 6 HOH B 22 522 56 HOH HOH . 
L 6 HOH B 23 523 49 HOH HOH . 
L 6 HOH B 24 524 39 HOH HOH . 
L 6 HOH B 25 525 47 HOH HOH . 
L 6 HOH B 26 526 60 HOH HOH . 
M 6 HOH C 1 801 43 HOH HOH . 
M 6 HOH C 2 802 16 HOH HOH . 
M 6 HOH C 3 803 26 HOH HOH . 
M 6 HOH C 4 804 11 HOH HOH . 
M 6 HOH C 5 805 42 HOH HOH . 
M 6 HOH C 6 806 21 HOH HOH . 
M 6 HOH C 7 807 5 HOH HOH . 
M 6 HOH C 8 808 61 HOH HOH . 
N 6 HOH D 1 801 63 HOH HOH . 
N 6 HOH D 2 802 44 HOH HOH . 
N 6 HOH D 3 803 17 HOH HOH . 
N 6 HOH D 4 804 25 HOH HOH . 
N 6 HOH D 5 805 45 HOH HOH . 
N 6 HOH D 6 806 9 HOH HOH . 
N 6 HOH D 7 807 51 HOH HOH . 
N 6 HOH D 8 808 46 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 P PG GCP . . . I 3 -42.057 15.502 19.881 1 32.48 ? PG GCP 401 B 1 
HETATM 2 O O1G GCP . . . I 3 -42.505 15.32 21.279 1 33.22 ? O1G GCP 401 B 1 
HETATM 3 O O2G GCP . . . I 3 -41.181 14.226 19.446 1 35.59 ? O2G GCP 401 B 1 
HETATM 4 O O3G GCP . . . I 3 -43.337 15.637 18.914 1 29.69 ? O3G GCP 401 B 1 
HETATM 5 C C3B GCP . . . I 3 -41.02 16.982 19.788 1 34.74 ? C3B GCP 401 B 1 
HETATM 6 P PB GCP . . . I 3 -41.122 17.756 18.154 1 33.58 ? PB GCP 401 B 1 
HETATM 7 O O1B GCP . . . I 3 -42.531 17.968 17.751 1 26.91 ? O1B GCP 401 B 1 
HETATM 8 O O2B GCP . . . I 3 -40.376 16.815 17.081 1 28.59 ? O2B GCP 401 B 1 
HETATM 9 O O3A GCP . . . I 3 -40.342 19.155 18.238 1 35.22 ? O3A GCP 401 B 1 
HETATM 10 P PA GCP . . . I 3 -41.119 20.538 18.502 1 32.3 ? PA GCP 401 B 1 
HETATM 11 O O1A GCP . . . I 3 -42.053 20.349 19.675 1 31.44 ? O1A GCP 401 B 1 
HETATM 12 O O2A GCP . . . I 3 -41.641 21.051 17.183 1 35.9 ? O2A GCP 401 B 1 
HETATM 13 O O5' GCP . . . I 3 -39.885 21.46 18.962 1 30.56 ? O5' GCP 401 B 1 
HETATM 14 C C5' GCP . . . I 3 -39.226 21.197 20.199 1 32.19 ? C5' GCP 401 B 1 
HETATM 15 C C4' GCP . . . I 3 -38.143 22.242 20.406 1 37.33 ? C4' GCP 401 B 1 
HETATM 16 O O4' GCP . . . I 3 -37.324 22.303 19.237 1 38.97 ? O4' GCP 401 B 1 
HETATM 17 C C3' GCP . . . I 3 -38.781 23.609 20.585 1 38.2 ? C3' GCP 401 B 1 
HETATM 18 O O3' GCP . . . I 3 -38.135 24.288 21.666 1 35.56 ? O3' GCP 401 B 1 
HETATM 19 C C2' GCP . . . I 3 -38.511 24.348 19.294 1 36.53 ? C2' GCP 401 B 1 
HETATM 20 O O2' GCP . . . I 3 -38.25 25.731 19.54 1 36.39 ? O2' GCP 401 B 1 
HETATM 21 C C1' GCP . . . I 3 -37.288 23.641 18.736 1 39.29 ? C1' GCP 401 B 1 
HETATM 22 N N9 GCP . . . I 3 -37.298 23.654 17.255 1 44.5 ? N9 GCP 401 B 1 
HETATM 23 C C8 GCP . . . I 3 -38.172 23.028 16.442 1 41.8 ? C8 GCP 401 B 1 
HETATM 24 N N7 GCP . . . I 3 -37.875 23.271 15.137 1 40.65 ? N7 GCP 401 B 1 
HETATM 25 C C5 GCP . . . I 3 -36.789 24.069 15.109 1 39.85 ? C5 GCP 401 B 1 
HETATM 26 C C6 GCP . . . I 3 -35.945 24.705 14.07 1 38.58 ? C6 GCP 401 B 1 
HETATM 27 O O6 GCP . . . I 3 -36.189 24.548 12.853 1 37.94 ? O6 GCP 401 B 1 
HETATM 28 N N1 GCP . . . I 3 -34.913 25.457 14.475 1 39.22 ? N1 GCP 401 B 1 
HETATM 29 C C2 GCP . . . I 3 -34.621 25.65 15.776 1 41.34 ? C2 GCP 401 B 1 
HETATM 30 N N2 GCP . . . I 3 -33.56 26.425 16.106 1 41.93 ? N2 GCP 401 B 1 
HETATM 31 N N3 GCP . . . I 3 -35.349 25.101 16.778 1 43.54 ? N3 GCP 401 B 1 
HETATM 32 C C4 GCP . . . I 3 -36.419 24.32 16.508 1 42.6 ? C4 GCP 401 B 1 
#
_model_server_stats.io_time_ms              12 
_model_server_stats.parse_time_ms           14 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           302 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           32 
#