data_1VFP
#
_model_server_result.job_id            Dkx2hnLwIIn2BqhOcdEkEg 
_model_server_result.datetime_utc      '2024-11-21 13:40:02' 
_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          1vfp 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"J","auth_seq_id":2001}' 
#
_entry.id    1VFP 
#
_exptl.entry_id    1VFP 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              505.208 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE 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          107.21 
_cell.angle_gamma         90 
_cell.entry_id            1VFP 
_cell.length_a            90.92 
_cell.length_b            123.62 
_cell.length_c            151.82 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1VFP 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_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 
_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
? 4 F N N 
? 4 J 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 876 A CYS 876 1_555 A SG CYS 888 A CYS 888 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
disulf ? disulf2 B SG CYS 876 B CYS 876 1_555 B SG CYS 888 B CYS 888 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? 
metalc ? metalc1 A O VAL 304 A VAL 304 1_555 C CA CA . A CA 995 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.759 ? 
metalc ? metalc2 A O ALA 305 A ALA 305 1_555 C CA CA . A CA 995 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.288 ? 
metalc ? metalc3 A O ILE 307 A ILE 307 1_555 C CA CA . A CA 995 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.442 ? 
metalc ? metalc4 A OE1 GLU 309 A GLU 309 1_555 C CA CA . A CA 995 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.995 ? 
metalc ? metalc5 A OE2 GLU 309 A GLU 309 1_555 C CA CA . A CA 995 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.468 ? 
metalc ? metalc6 A OD2 ASP 351 A ASP 351 1_555 E MG MG . A MG 997 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.399 ? 
metalc ? metalc7 A O THR 353 A THR 353 1_555 E MG MG . A MG 997 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.163 ? 
metalc ? metalc8 A OD1 ASP 703 A ASP 703 1_555 E MG MG . A MG 997 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.132 ? 
metalc ? metalc9 A OD1 ASN 768 A ASN 768 1_555 D CA CA . A CA 996 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.531 ? 
metalc ? metalc10 A OE2 GLU 771 A GLU 771 1_555 D CA CA . A CA 996 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.411 ? 
metalc ? metalc11 A OD1 ASN 796 A ASN 796 1_555 C CA CA . A CA 995 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.375 ? 
metalc ? metalc12 A OG1 THR 799 A THR 799 1_555 D CA CA . A CA 996 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.417 ? 
metalc ? metalc13 A OD2 ASP 800 A ASP 800 1_555 C CA CA . A CA 995 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.327 ? 
metalc ? metalc14 A OD1 ASP 800 A ASP 800 1_555 D CA CA . A CA 996 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.262 ? 
metalc ? metalc15 A OE2 GLU 908 A GLU 908 1_555 D CA CA . A CA 996 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.509 ? 
metalc ? metalc16 A OE1 GLU 908 A GLU 908 1_555 D CA CA . A CA 996 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.198 ? 
metalc ? metalc17 D CA CA . A CA 996 1_555 K O HOH . A HOH 1013 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.388 ? 
metalc ? metalc18 D CA CA . A CA 996 1_555 K O HOH . A HOH 1014 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.654 ? 
metalc ? metalc19 E MG MG . A MG 997 1_555 F O2G ACP . A ACP 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.164 ? 
metalc ? metalc20 E MG MG . A MG 997 1_555 K O HOH . A HOH 1011 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.46 ? 
metalc ? metalc21 E MG MG . A MG 997 1_555 K O HOH . A HOH 1012 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.982 ? 
metalc ? metalc22 B O VAL 304 B VAL 304 1_555 G CA CA . B CA 995 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.703 ? 
metalc ? metalc23 B O ALA 305 B ALA 305 1_555 G CA CA . B CA 995 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.212 ? 
metalc ? metalc24 B O ILE 307 B ILE 307 1_555 G CA CA . B CA 995 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.455 ? 
metalc ? metalc25 B OE2 GLU 309 B GLU 309 1_555 G CA CA . B CA 995 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.495 ? 
metalc ? metalc26 B OE1 GLU 309 B GLU 309 1_555 G CA CA . B CA 995 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.078 ? 
metalc ? metalc27 B OD2 ASP 351 B ASP 351 1_555 I MG MG . B MG 997 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.352 ? 
metalc ? metalc28 B O THR 353 B THR 353 1_555 I MG MG . B MG 997 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.171 ? 
metalc ? metalc29 B OD1 ASP 703 B ASP 703 1_555 I MG MG . B MG 997 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.092 ? 
metalc ? metalc30 B OD1 ASN 768 B ASN 768 1_555 H CA CA . B CA 996 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.51 ? 
metalc ? metalc31 B OE2 GLU 771 B GLU 771 1_555 H CA CA . B CA 996 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.373 ? 
metalc ? metalc32 B OD1 ASN 796 B ASN 796 1_555 G CA CA . B CA 995 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.363 ? 
metalc ? metalc33 B OG1 THR 799 B THR 799 1_555 H CA CA . B CA 996 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.461 ? 
metalc ? metalc34 B OD2 ASP 800 B ASP 800 1_555 G CA CA . B CA 995 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.37 ? 
metalc ? metalc35 B OD1 ASP 800 B ASP 800 1_555 H CA CA . B CA 996 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.297 ? 
metalc ? metalc36 B OE2 GLU 908 B GLU 908 1_555 H CA CA . B CA 996 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.522 ? 
metalc ? metalc37 B OE1 GLU 908 B GLU 908 1_555 H CA CA . B CA 996 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.203 ? 
metalc ? metalc38 H CA CA . B CA 996 1_555 L O HOH . B HOH 2013 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.447 ? 
metalc ? metalc39 H CA CA . B CA 996 1_555 L O HOH . B HOH 2014 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.628 ? 
metalc ? metalc40 I MG MG . B MG 997 1_555 J O2G ACP . B ACP 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.135 ? 
metalc ? metalc41 I MG MG . B MG 997 1_555 L O HOH . B HOH 2011 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.515 ? 
metalc ? metalc42 I MG MG . B MG 997 1_555 L O HOH . B HOH 2012 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.961 ? 
#
_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                     1VFP 
_atom_sites.fract_transf_matrix[1][1]    0.010999 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.003407 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.008089 
_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]    0.006895 
_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
C 2 CA A 1 995 995 CA CA . 
D 2 CA A 1 996 996 CA CA . 
E 3 MG A 1 997 997 MG MG . 
F 4 ACP A 1 1001 1001 ACP ACP . 
G 2 CA B 1 995 995 CA CA . 
H 2 CA B 1 996 996 CA CA . 
I 3 MG B 1 997 997 MG MG . 
J 4 ACP B 1 2001 2001 ACP ACP . 
K 5 HOH A 1 1011 1011 HOH HOH . 
K 5 HOH A 2 1012 1012 HOH HOH . 
K 5 HOH A 3 1013 1013 HOH HOH . 
K 5 HOH A 4 1014 1014 HOH HOH . 
L 5 HOH B 1 2011 2011 HOH HOH . 
L 5 HOH B 2 2012 2012 HOH HOH . 
L 5 HOH B 3 2013 2013 HOH HOH . 
L 5 HOH B 4 2014 2014 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 . . . J 4 32.748 6.385 -57.128 1 29.27 ? PG ACP 2001 B 1 
HETATM 2 O O1G ACP . . . J 4 33.957 5.492 -57.464 1 20.95 ? O1G ACP 2001 B 1 
HETATM 3 O O2G ACP . . . J 4 32.058 5.927 -55.856 1 18.77 ? O2G ACP 2001 B 1 
HETATM 4 O O3G ACP . . . J 4 33.067 7.907 -57.167 1 25.72 ? O3G ACP 2001 B 1 
HETATM 5 P PB ACP . . . J 4 31.874 6.239 -60.086 1 21.58 ? PB ACP 2001 B 1 
HETATM 6 O O1B ACP . . . J 4 30.532 5.865 -60.63 1 17.34 ? O1B ACP 2001 B 1 
HETATM 7 O O2B ACP . . . J 4 32.487 7.412 -60.7 1 21.43 ? O2B ACP 2001 B 1 
HETATM 8 C C3B ACP . . . J 4 31.532 6.186 -58.367 1 23.31 ? C3B ACP 2001 B 1 
HETATM 9 P PA ACP . . . J 4 32.514 3.595 -61.341 1 19.34 ? PA ACP 2001 B 1 
HETATM 10 O O1A ACP . . . J 4 31.295 2.953 -60.68 1 16.2 ? O1A ACP 2001 B 1 
HETATM 11 O O2A ACP . . . J 4 33.753 2.765 -61.377 1 21.22 ? O2A ACP 2001 B 1 
HETATM 12 O O3A ACP . . . J 4 32.845 5.021 -60.656 1 24.45 ? O3A ACP 2001 B 1 
HETATM 13 O O5' ACP . . . J 4 31.983 4.118 -62.746 1 19.25 ? O5' ACP 2001 B 1 
HETATM 14 C C5' ACP . . . J 4 32.977 4.778 -63.53 1 23.3 ? C5' ACP 2001 B 1 
HETATM 15 C C4' ACP . . . J 4 32.694 5.715 -64.708 1 24.84 ? C4' ACP 2001 B 1 
HETATM 16 O O4' ACP . . . J 4 31.7 5.117 -65.496 1 22.03 ? O4' ACP 2001 B 1 
HETATM 17 C C3' ACP . . . J 4 31.889 6.75 -63.927 1 27.04 ? C3' ACP 2001 B 1 
HETATM 18 O O3' ACP . . . J 4 32.711 7.678 -63.266 1 33.15 ? O3' ACP 2001 B 1 
HETATM 19 C C2' ACP . . . J 4 30.944 7.309 -64.991 1 24.2 ? C2' ACP 2001 B 1 
HETATM 20 O O2' ACP . . . J 4 31.619 8.298 -65.762 1 24.35 ? O2' ACP 2001 B 1 
HETATM 21 C C1' ACP . . . J 4 30.628 6.056 -65.686 1 22.41 ? C1' ACP 2001 B 1 
HETATM 22 N N9 ACP . . . J 4 29.278 5.468 -65.257 1 18.71 ? N9 ACP 2001 B 1 
HETATM 23 C C8 ACP . . . J 4 28.722 5.262 -64.05 1 20.69 ? C8 ACP 2001 B 1 
HETATM 24 N N7 ACP . . . J 4 27.503 4.731 -64.048 1 20.7 ? N7 ACP 2001 B 1 
HETATM 25 C C5 ACP . . . J 4 27.269 4.588 -65.336 1 16.74 ? C5 ACP 2001 B 1 
HETATM 26 C C6 ACP . . . J 4 26.165 4.083 -66.105 1 17.25 ? C6 ACP 2001 B 1 
HETATM 27 N N6 ACP . . . J 4 25.043 3.617 -65.505 1 19.17 ? N6 ACP 2001 B 1 
HETATM 28 N N1 ACP . . . J 4 26.215 4.062 -67.483 1 16.2 ? N1 ACP 2001 B 1 
HETATM 29 C C2 ACP . . . J 4 27.314 4.526 -68.127 1 16.2 ? C2 ACP 2001 B 1 
HETATM 30 N N3 ACP . . . J 4 28.4 5.021 -67.482 1 18.78 ? N3 ACP 2001 B 1 
HETATM 31 C C4 ACP . . . J 4 28.337 5.033 -66.121 1 16.2 ? C4 ACP 2001 B 1 
#
_model_server_stats.io_time_ms              68 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    28 
_model_server_stats.query_time_ms           296 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           31 
#