data_4GRA
#
_model_server_result.job_id            elgYt_y52LSbHeU1zBZHiw 
_model_server_result.datetime_utc      '2024-12-22 01:10:43' 
_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          4gra 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":301}' 
#
_entry.id    4GRA 
#
_exptl.entry_id    4GRA 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              427.201 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "ADENOSINE-3'-5'-DIPHOSPHATE" 
_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          92.12 
_cell.angle_gamma         90 
_cell.entry_id            4GRA 
_cell.length_a            48.296 
_cell.length_b            122.428 
_cell.length_c            55.021 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4GRA 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
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 monomeric 1 author_and_software_defined_assembly 1 
PISA monomeric 1 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,C,E 1 1 
B,D,F 2 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
? 2 C N N 
? 2 D N N 
#
_chem_comp.formula           'C10 H15 N5 O10 P2' 
_chem_comp.formula_weight    427.201 
_chem_comp.id                A3P 
_chem_comp.mon_nstd_flag     n 
_chem_comp.name              "ADENOSINE-3'-5'-DIPHOSPHATE" 
_chem_comp.type              'rna 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
P1 O1P A3P doub 1 n n 
P1 O2P A3P sing 2 n n 
P1 O3P A3P sing 3 n n 
P1 O3' A3P sing 4 n n 
O2P HOP2 A3P sing 5 n n 
O3P HOP3 A3P sing 6 n n 
P2 O4P A3P doub 7 n n 
P2 O5P A3P sing 8 n n 
P2 O6P A3P sing 9 n n 
P2 O5' A3P sing 10 n n 
O5P HOP5 A3P sing 11 n n 
O6P HOP6 A3P sing 12 n n 
O5' C5' A3P sing 13 n n 
C5' C4' A3P sing 14 n n 
C5' "H5'1" A3P sing 15 n n 
C5' "H5'2" A3P sing 16 n n 
C4' O4' A3P sing 17 n n 
C4' C3' A3P sing 18 n n 
C4' H4' A3P sing 19 n n 
O4' C1' A3P sing 20 n n 
C3' O3' A3P sing 21 n n 
C3' C2' A3P sing 22 n n 
C3' H3' A3P sing 23 n n 
C2' O2' A3P sing 24 n n 
C2' C1' A3P sing 25 n n 
C2' H2' A3P sing 26 n n 
O2' HO2' A3P sing 27 n n 
C1' N9 A3P sing 28 n n 
C1' H1' A3P sing 29 n n 
N9 C8 A3P sing 30 n y 
N9 C4 A3P sing 31 n y 
C8 N7 A3P doub 32 n y 
C8 H8 A3P sing 33 n n 
N7 C5 A3P sing 34 n y 
C5 C6 A3P sing 35 n y 
C5 C4 A3P doub 36 n y 
C6 N6 A3P sing 37 n n 
C6 N1 A3P doub 38 n y 
N6 HN61 A3P sing 39 n n 
N6 HN62 A3P sing 40 n n 
N1 C2 A3P sing 41 n y 
C2 N3 A3P doub 42 n y 
C2 H2 A3P sing 43 n n 
N3 C4 A3P sing 44 n y 
#
_atom_sites.entry_id                     4GRA 
_atom_sites.fract_transf_matrix[1][1]    0.020706 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000766 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.008168 
_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]    0.018187 
_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 A3P A 1 301 1 A3P A3P . 
D 2 A3P B 1 301 1 A3P A3P . 
E 3 HOH A 1 401 2 HOH HOH . 
E 3 HOH A 2 402 3 HOH HOH . 
E 3 HOH A 3 403 7 HOH HOH . 
E 3 HOH A 4 404 8 HOH HOH . 
E 3 HOH A 5 405 9 HOH HOH . 
E 3 HOH A 6 406 10 HOH HOH . 
E 3 HOH A 7 407 16 HOH HOH . 
E 3 HOH A 8 408 18 HOH HOH . 
E 3 HOH A 9 409 19 HOH HOH . 
E 3 HOH A 10 410 20 HOH HOH . 
E 3 HOH A 11 411 25 HOH HOH . 
E 3 HOH A 12 412 26 HOH HOH . 
E 3 HOH A 13 413 27 HOH HOH . 
E 3 HOH A 14 414 29 HOH HOH . 
E 3 HOH A 15 415 33 HOH HOH . 
E 3 HOH A 16 416 34 HOH HOH . 
E 3 HOH A 17 417 37 HOH HOH . 
E 3 HOH A 18 418 39 HOH HOH . 
E 3 HOH A 19 419 40 HOH HOH . 
E 3 HOH A 20 420 41 HOH HOH . 
E 3 HOH A 21 421 43 HOH HOH . 
E 3 HOH A 22 422 44 HOH HOH . 
E 3 HOH A 23 423 47 HOH HOH . 
E 3 HOH A 24 424 56 HOH HOH . 
E 3 HOH A 25 425 57 HOH HOH . 
E 3 HOH A 26 426 58 HOH HOH . 
E 3 HOH A 27 427 59 HOH HOH . 
E 3 HOH A 28 428 60 HOH HOH . 
E 3 HOH A 29 429 61 HOH HOH . 
E 3 HOH A 30 430 62 HOH HOH . 
E 3 HOH A 31 431 63 HOH HOH . 
E 3 HOH A 32 432 64 HOH HOH . 
E 3 HOH A 33 433 65 HOH HOH . 
E 3 HOH A 34 434 68 HOH HOH . 
E 3 HOH A 35 435 70 HOH HOH . 
E 3 HOH A 36 436 71 HOH HOH . 
E 3 HOH A 37 437 72 HOH HOH . 
E 3 HOH A 38 438 73 HOH HOH . 
E 3 HOH A 39 439 74 HOH HOH . 
E 3 HOH A 40 440 75 HOH HOH . 
E 3 HOH A 41 441 77 HOH HOH . 
E 3 HOH A 42 442 78 HOH HOH . 
E 3 HOH A 43 443 79 HOH HOH . 
F 3 HOH B 1 401 1 HOH HOH . 
F 3 HOH B 2 402 4 HOH HOH . 
F 3 HOH B 3 403 5 HOH HOH . 
F 3 HOH B 4 404 6 HOH HOH . 
F 3 HOH B 5 405 11 HOH HOH . 
F 3 HOH B 6 406 12 HOH HOH . 
F 3 HOH B 7 407 13 HOH HOH . 
F 3 HOH B 8 408 14 HOH HOH . 
F 3 HOH B 9 409 15 HOH HOH . 
F 3 HOH B 10 410 17 HOH HOH . 
F 3 HOH B 11 411 21 HOH HOH . 
F 3 HOH B 12 412 22 HOH HOH . 
F 3 HOH B 13 413 23 HOH HOH . 
F 3 HOH B 14 414 24 HOH HOH . 
F 3 HOH B 15 415 28 HOH HOH . 
F 3 HOH B 16 416 30 HOH HOH . 
F 3 HOH B 17 417 31 HOH HOH . 
F 3 HOH B 18 418 32 HOH HOH . 
F 3 HOH B 19 419 35 HOH HOH . 
F 3 HOH B 20 420 36 HOH HOH . 
F 3 HOH B 21 421 38 HOH HOH . 
F 3 HOH B 22 422 42 HOH HOH . 
F 3 HOH B 23 423 45 HOH HOH . 
F 3 HOH B 24 424 46 HOH HOH . 
F 3 HOH B 25 425 48 HOH HOH . 
F 3 HOH B 26 426 49 HOH HOH . 
F 3 HOH B 27 427 50 HOH HOH . 
F 3 HOH B 28 428 51 HOH HOH . 
F 3 HOH B 29 429 52 HOH HOH . 
F 3 HOH B 30 430 53 HOH HOH . 
F 3 HOH B 31 431 54 HOH HOH . 
F 3 HOH B 32 432 55 HOH HOH . 
F 3 HOH B 33 433 66 HOH HOH . 
F 3 HOH B 34 434 67 HOH HOH . 
F 3 HOH B 35 435 69 HOH HOH . 
F 3 HOH B 36 436 76 HOH HOH . 
F 3 HOH B 37 437 80 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 P1 A3P . . . D 2 0.027 -6.851 -2.623 1 30.92 ? P1 A3P 301 B 1 
HETATM 2 O O1P A3P . . . D 2 -1.447 -6.562 -2.484 1 31.82 ? O1P A3P 301 B 1 
HETATM 3 O O2P A3P . . . D 2 0.85 -5.714 -2.073 1 33.19 ? O2P A3P 301 B 1 
HETATM 4 O O3P A3P . . . D 2 0.504 -7.318 -3.974 1 30.26 ? O3P A3P 301 B 1 
HETATM 5 P P2 A3P . . . D 2 2.586 -13.722 -0.591 1 29.84 ? P2 A3P 301 B 1 
HETATM 6 O O4P A3P . . . D 2 1.521 -14.697 -0.154 1 29.52 ? O4P A3P 301 B 1 
HETATM 7 O O5P A3P . . . D 2 3.015 -13.829 -2.033 1 29.27 ? O5P A3P 301 B 1 
HETATM 8 O O6P A3P . . . D 2 3.757 -13.608 0.357 1 29.21 ? O6P A3P 301 B 1 
HETATM 9 O O5' A3P . . . D 2 1.806 -12.335 -0.428 1 29.28 ? O5' A3P 301 B 1 
HETATM 10 C C5' A3P . . . D 2 2.301 -11.139 -1.026 1 30.18 ? C5' A3P 301 B 1 
HETATM 11 C C4' A3P . . . D 2 1.312 -10.004 -0.764 1 29.32 ? C4' A3P 301 B 1 
HETATM 12 O O4' A3P . . . D 2 1.433 -9.538 0.58 1 30.39 ? O4' A3P 301 B 1 
HETATM 13 C C3' A3P . . . D 2 1.579 -8.79 -1.622 1 29.83 ? C3' A3P 301 B 1 
HETATM 14 O O3' A3P . . . D 2 0.328 -8.096 -1.654 1 30.26 ? O3' A3P 301 B 1 
HETATM 15 C C2' A3P . . . D 2 2.6 -8.037 -0.788 1 30.91 ? C2' A3P 301 B 1 
HETATM 16 O O2' A3P . . . D 2 2.815 -6.684 -1.212 1 29.49 ? O2' A3P 301 B 1 
HETATM 17 C C1' A3P . . . D 2 1.962 -8.202 0.594 1 32.39 ? C1' A3P 301 B 1 
HETATM 18 N N9 A3P . . . D 2 2.88 -8.097 1.756 1 34.64 ? N9 A3P 301 B 1 
HETATM 19 C C8 A3P . . . D 2 4.122 -8.622 1.869 1 35.64 ? C8 A3P 301 B 1 
HETATM 20 N N7 A3P . . . D 2 4.673 -8.347 3.077 1 34.71 ? N7 A3P 301 B 1 
HETATM 21 C C5 A3P . . . D 2 3.765 -7.632 3.762 1 35.38 ? C5 A3P 301 B 1 
HETATM 22 C C6 A3P . . . D 2 3.706 -7.008 5.1 1 36.28 ? C6 A3P 301 B 1 
HETATM 23 N N6 A3P . . . D 2 4.749 -7.115 5.958 1 35.59 ? N6 A3P 301 B 1 
HETATM 24 N N1 A3P . . . D 2 2.572 -6.34 5.423 1 38.21 ? N1 A3P 301 B 1 
HETATM 25 C C2 A3P . . . D 2 1.525 -6.224 4.562 1 38.13 ? C2 A3P 301 B 1 
HETATM 26 N N3 A3P . . . D 2 1.511 -6.765 3.333 1 35.13 ? N3 A3P 301 B 1 
HETATM 27 C C4 A3P . . . D 2 2.583 -7.468 2.892 1 35.37 ? C4 A3P 301 B 1 
#
_model_server_stats.io_time_ms              65 
_model_server_stats.parse_time_ms           14 
_model_server_stats.create_model_time_ms    21 
_model_server_stats.query_time_ms           372 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           27 
#