data_3JVV
#
_model_server_result.job_id            HyMHpNF3yETLHuAj7VKRGA 
_model_server_result.datetime_utc      '2025-06-29 03:17:45' 
_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          3jvv 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":400}' 
#
_entry.id    3JVV 
#
_exptl.entry_id    3JVV 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              505.208 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER' 
_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         90 
_cell.entry_id            3JVV 
_cell.length_a            108.483 
_cell.length_b            119.552 
_cell.length_c            185.535 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3JVV 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        20 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 2 2 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    hexameric 
_pdbx_struct_assembly.oligomeric_count      6 
_pdbx_struct_assembly.details               author_and_software_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 
_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' 3_455 -x-1,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 -108.483 0 92.7675 
#
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 G N N 
? 2 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 137 A SER 137 1_555 E MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.742 ? 
metalc ? metalc2 D O2G ACP . A ACP 400 1_555 E MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.831 ? 
metalc ? metalc3 D O1B ACP . A ACP 400 1_555 E MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.352 ? 
metalc ? metalc4 B OG SER 137 B SER 137 1_555 H MG MG . B MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.433 ? 
metalc ? metalc5 L O HOH . B HOH 362 1_555 H MG MG . B MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.886 ? 
metalc ? metalc6 G O1B ACP . B ACP 400 1_555 H MG MG . B MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.756 ? 
metalc ? metalc7 G O2G ACP . B ACP 400 1_555 H MG MG . B MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.854 ? 
metalc ? metalc8 C OG SER 137 C SER 137 1_555 J MG MG . C MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.606 ? 
metalc ? metalc9 I O1B ACP . C ACP 400 1_555 J MG MG . C MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.825 ? 
#
_chem_comp.formula           'C11 H18 N5 O12 P3' 
_chem_comp.formula_weight    505.208 
_chem_comp.id                ACP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     "ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE" 
#
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 ACP doub 1 n n 
PG O2G ACP sing 2 n n 
PG O3G ACP sing 3 n n 
PG C3B ACP sing 4 n n 
O2G HOG2 ACP sing 5 n n 
O3G HOG3 ACP sing 6 n n 
PB O1B ACP doub 7 n n 
PB O2B ACP sing 8 n n 
PB C3B ACP sing 9 n n 
PB O3A ACP sing 10 n n 
O2B HOB2 ACP sing 11 n n 
C3B H3B1 ACP sing 12 n n 
C3B H3B2 ACP sing 13 n n 
PA O1A ACP doub 14 n n 
PA O2A ACP sing 15 n n 
PA O3A ACP sing 16 n n 
PA O5' ACP sing 17 n n 
O2A HOA2 ACP sing 18 n n 
O5' C5' ACP sing 19 n n 
C5' C4' ACP sing 20 n n 
C5' "H5'1" ACP sing 21 n n 
C5' "H5'2" ACP sing 22 n n 
C4' O4' ACP sing 23 n n 
C4' C3' ACP sing 24 n n 
C4' H4' ACP sing 25 n n 
O4' C1' ACP sing 26 n n 
C3' O3' ACP sing 27 n n 
C3' C2' ACP sing 28 n n 
C3' H3' ACP sing 29 n n 
O3' HO3' ACP sing 30 n n 
C2' O2' ACP sing 31 n n 
C2' C1' ACP sing 32 n n 
C2' H2' ACP sing 33 n n 
O2' HO2' ACP sing 34 n n 
C1' N9 ACP sing 35 n n 
C1' H1' ACP sing 36 n n 
N9 C8 ACP sing 37 n y 
N9 C4 ACP sing 38 n y 
C8 N7 ACP doub 39 n y 
C8 H8 ACP sing 40 n n 
N7 C5 ACP sing 41 n y 
C5 C6 ACP sing 42 n y 
C5 C4 ACP doub 43 n y 
C6 N6 ACP sing 44 n n 
C6 N1 ACP doub 45 n y 
N6 HN61 ACP sing 46 n n 
N6 HN62 ACP sing 47 n n 
N1 C2 ACP sing 48 n y 
C2 N3 ACP doub 49 n y 
C2 H2 ACP sing 50 n n 
N3 C4 ACP sing 51 n y 
#
_atom_sites.entry_id                     3JVV 
_atom_sites.fract_transf_matrix[1][1]    0.009218 
_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]    0.008365 
_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]    0.00539 
_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 ACP A 1 400 400 ACP ACP . 
E 3 MG A 1 401 401 MG MG . 
F 4 CIT A 1 357 1 CIT CIT . 
G 2 ACP B 1 400 400 ACP ACP . 
H 3 MG B 1 401 401 MG MG . 
I 2 ACP C 1 400 400 ACP ACP . 
J 3 MG C 1 401 401 MG MG . 
K 5 HOH A 1 358 1 HOH HOH . 
K 5 HOH A 2 359 3 HOH HOH . 
K 5 HOH A 3 360 4 HOH HOH . 
K 5 HOH A 4 361 5 HOH HOH . 
K 5 HOH A 5 362 9 HOH HOH . 
K 5 HOH A 6 363 10 HOH HOH . 
K 5 HOH A 7 364 11 HOH HOH . 
K 5 HOH A 8 365 12 HOH HOH . 
K 5 HOH A 9 366 22 HOH HOH . 
K 5 HOH A 10 367 24 HOH HOH . 
K 5 HOH A 11 368 25 HOH HOH . 
K 5 HOH A 12 369 27 HOH HOH . 
K 5 HOH A 13 370 29 HOH HOH . 
K 5 HOH A 14 371 32 HOH HOH . 
K 5 HOH A 15 372 37 HOH HOH . 
K 5 HOH A 16 373 38 HOH HOH . 
K 5 HOH A 17 374 39 HOH HOH . 
K 5 HOH A 18 375 41 HOH HOH . 
K 5 HOH A 19 376 49 HOH HOH . 
K 5 HOH A 20 377 51 HOH HOH . 
K 5 HOH A 21 378 52 HOH HOH . 
K 5 HOH A 22 379 53 HOH HOH . 
K 5 HOH A 23 380 56 HOH HOH . 
K 5 HOH A 24 381 57 HOH HOH . 
K 5 HOH A 25 382 61 HOH HOH . 
K 5 HOH A 26 383 64 HOH HOH . 
K 5 HOH A 27 384 66 HOH HOH . 
K 5 HOH A 28 385 69 HOH HOH . 
K 5 HOH A 29 386 76 HOH HOH . 
K 5 HOH A 30 387 82 HOH HOH . 
K 5 HOH A 31 388 85 HOH HOH . 
K 5 HOH A 32 389 88 HOH HOH . 
L 5 HOH B 1 357 2 HOH HOH . 
L 5 HOH B 2 358 6 HOH HOH . 
L 5 HOH B 3 359 7 HOH HOH . 
L 5 HOH B 4 360 13 HOH HOH . 
L 5 HOH B 5 361 14 HOH HOH . 
L 5 HOH B 6 362 18 HOH HOH . 
L 5 HOH B 7 363 20 HOH HOH . 
L 5 HOH B 8 364 26 HOH HOH . 
L 5 HOH B 9 365 30 HOH HOH . 
L 5 HOH B 10 366 34 HOH HOH . 
L 5 HOH B 11 367 36 HOH HOH . 
L 5 HOH B 12 368 40 HOH HOH . 
L 5 HOH B 13 369 43 HOH HOH . 
L 5 HOH B 14 370 44 HOH HOH . 
L 5 HOH B 15 371 45 HOH HOH . 
L 5 HOH B 16 372 46 HOH HOH . 
L 5 HOH B 17 373 48 HOH HOH . 
L 5 HOH B 18 374 54 HOH HOH . 
L 5 HOH B 19 375 55 HOH HOH . 
L 5 HOH B 20 376 60 HOH HOH . 
L 5 HOH B 21 377 62 HOH HOH . 
L 5 HOH B 22 378 68 HOH HOH . 
L 5 HOH B 23 379 70 HOH HOH . 
L 5 HOH B 24 380 73 HOH HOH . 
L 5 HOH B 25 381 74 HOH HOH . 
L 5 HOH B 26 382 77 HOH HOH . 
L 5 HOH B 27 383 78 HOH HOH . 
L 5 HOH B 28 384 80 HOH HOH . 
L 5 HOH B 29 385 86 HOH HOH . 
M 5 HOH C 1 357 8 HOH HOH . 
M 5 HOH C 2 358 15 HOH HOH . 
M 5 HOH C 3 359 16 HOH HOH . 
M 5 HOH C 4 360 17 HOH HOH . 
M 5 HOH C 5 361 19 HOH HOH . 
M 5 HOH C 6 362 21 HOH HOH . 
M 5 HOH C 7 363 23 HOH HOH . 
M 5 HOH C 8 364 28 HOH HOH . 
M 5 HOH C 9 365 31 HOH HOH . 
M 5 HOH C 10 366 33 HOH HOH . 
M 5 HOH C 11 367 35 HOH HOH . 
M 5 HOH C 12 368 42 HOH HOH . 
M 5 HOH C 13 369 47 HOH HOH . 
M 5 HOH C 14 370 50 HOH HOH . 
M 5 HOH C 15 371 58 HOH HOH . 
M 5 HOH C 16 372 59 HOH HOH . 
M 5 HOH C 17 373 63 HOH HOH . 
M 5 HOH C 18 374 65 HOH HOH . 
M 5 HOH C 19 375 67 HOH HOH . 
M 5 HOH C 20 376 71 HOH HOH . 
M 5 HOH C 21 377 72 HOH HOH . 
M 5 HOH C 22 378 75 HOH HOH . 
M 5 HOH C 23 379 79 HOH HOH . 
M 5 HOH C 24 380 81 HOH HOH . 
M 5 HOH C 25 381 83 HOH HOH . 
M 5 HOH C 26 382 84 HOH HOH . 
M 5 HOH C 27 383 87 HOH HOH . 
M 5 HOH C 28 384 89 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 ACP . . . D 2 -20.908 24.108 32.222 1 68.48 ? PG ACP 400 A 1 
HETATM 2 O O1G ACP . . . D 2 -21.082 22.77 32.901 1 67.39 ? O1G ACP 400 A 1 
HETATM 3 O O2G ACP . . . D 2 -22.02 24.471 31.251 1 68.75 ? O2G ACP 400 A 1 
HETATM 4 O O3G ACP . . . D 2 -20.522 25.272 33.115 1 68.01 ? O3G ACP 400 A 1 
HETATM 5 P PB ACP . . . D 2 -19.692 22.417 30.063 1 68.29 ? PB ACP 400 A 1 
HETATM 6 O O1B ACP . . . D 2 -20.531 22.804 28.85 1 68.43 ? O1B ACP 400 A 1 
HETATM 7 O O2B ACP . . . D 2 -20.106 21.244 30.916 1 68.27 ? O2B ACP 400 A 1 
HETATM 8 C C3B ACP . . . D 2 -19.479 23.875 31.117 1 68.28 ? C3B ACP 400 A 1 
HETATM 9 P PA ACP . . . D 2 -17.713 23.117 28.329 1 68.14 ? PA ACP 400 A 1 
HETATM 10 O O1A ACP . . . D 2 -17.925 24.485 28.896 1 68.88 ? O1A ACP 400 A 1 
HETATM 11 O O2A ACP . . . D 2 -18.518 22.746 27.113 1 68.37 ? O2A ACP 400 A 1 
HETATM 12 O O3A ACP . . . D 2 -18.223 22.102 29.479 1 68.61 ? O3A ACP 400 A 1 
HETATM 13 O O5' ACP . . . D 2 -16.143 22.788 28.167 1 69.54 ? O5' ACP 400 A 1 
HETATM 14 C C5' ACP . . . D 2 -15.311 22.969 29.317 1 71.11 ? C5' ACP 400 A 1 
HETATM 15 C C4' ACP . . . D 2 -13.821 22.805 29.037 1 72.07 ? C4' ACP 400 A 1 
HETATM 16 O O4' ACP . . . D 2 -13.517 21.453 28.668 1 72.31 ? O4' ACP 400 A 1 
HETATM 17 C C3' ACP . . . D 2 -13.365 23.763 27.938 1 72.3 ? C3' ACP 400 A 1 
HETATM 18 O O3' ACP . . . D 2 -12.082 24.29 28.285 1 72.74 ? O3' ACP 400 A 1 
HETATM 19 C C2' ACP . . . D 2 -13.263 22.826 26.739 1 72.59 ? C2' ACP 400 A 1 
HETATM 20 O O2' ACP . . . D 2 -12.187 23.169 25.86 1 72.52 ? O2' ACP 400 A 1 
HETATM 21 C C1' ACP . . . D 2 -12.899 21.496 27.384 1 72.63 ? C1' ACP 400 A 1 
HETATM 22 N N9 ACP . . . D 2 -13.459 20.414 26.539 1 72.91 ? N9 ACP 400 A 1 
HETATM 23 C C8 ACP . . . D 2 -14.758 20.287 26.203 1 72.91 ? C8 ACP 400 A 1 
HETATM 24 N N7 ACP . . . D 2 -14.971 19.203 25.419 1 72.9 ? N7 ACP 400 A 1 
HETATM 25 C C5 ACP . . . D 2 -13.773 18.615 25.242 1 73.04 ? C5 ACP 400 A 1 
HETATM 26 C C6 ACP . . . D 2 -13.277 17.42 24.523 1 72.91 ? C6 ACP 400 A 1 
HETATM 27 N N6 ACP . . . D 2 -14.123 16.628 23.825 1 72.69 ? N6 ACP 400 A 1 
HETATM 28 N N1 ACP . . . D 2 -11.954 17.156 24.589 1 72.94 ? N1 ACP 400 A 1 
HETATM 29 C C2 ACP . . . D 2 -11.109 17.939 25.283 1 73.18 ? C2 ACP 400 A 1 
HETATM 30 N N3 ACP . . . D 2 -11.486 19.038 25.964 1 73.37 ? N3 ACP 400 A 1 
HETATM 31 C C4 ACP . . . D 2 -12.782 19.417 25.98 1 73.03 ? C4 ACP 400 A 1 
#
_model_server_stats.io_time_ms              67 
_model_server_stats.parse_time_ms           17 
_model_server_stats.create_model_time_ms    35 
_model_server_stats.query_time_ms           545 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           31 
#