data_3C51
#
_model_server_result.job_id            l06fSKRZsMYRjNVpXupfcg 
_model_server_result.datetime_utc      '2024-11-05 23:06:38' 
_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          3c51 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"M","auth_seq_id":562}' 
#
_entry.id    3C51 
#
_exptl.entry_id    3C51 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              427.201 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "ADENOSINE-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          90 
_cell.angle_gamma         90 
_cell.entry_id            3C51 
_cell.length_a            58.657 
_cell.length_b            92.527 
_cell.length_c            259.383 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3C51 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_pdbx_struct_assembly.details               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 
#
_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 H N N 
? 4 M 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 OD1 ASP 332 A ASP 332 1_555 D MG MG . A MG 564 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.168 ? 
metalc ? metalc2 H O2A ADP . A ADP 562 1_555 C MG MG . A MG 563 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.274 ? 
metalc ? metalc3 H O3B ADP . A ADP 562 1_555 C MG MG . A MG 563 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.43 ? 
metalc ? metalc4 M O3B ADP . B ADP 562 1_555 J MG MG . B MG 563 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.488 ? 
metalc ? metalc5 M O2A ADP . B ADP 562 1_555 J MG MG . B MG 563 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.278 ? 
metalc ? metalc6 M O2B ADP . B ADP 562 1_555 K MG MG . B MG 564 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.878 ? 
#
_chem_comp.formula           'C10 H15 N5 O10 P2' 
_chem_comp.formula_weight    427.201 
_chem_comp.id                ADP 
_chem_comp.mon_nstd_flag     n 
_chem_comp.name              "ADENOSINE-5'-DIPHOSPHATE" 
_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
PB O1B ADP doub 1 n n 
PB O2B ADP sing 2 n n 
PB O3B ADP sing 3 n n 
PB O3A ADP sing 4 n n 
O2B HOB2 ADP sing 5 n n 
O3B HOB3 ADP sing 6 n n 
PA O1A ADP doub 7 n n 
PA O2A ADP sing 8 n n 
PA O3A ADP sing 9 n n 
PA O5' ADP sing 10 n n 
O2A HOA2 ADP sing 11 n n 
O5' C5' ADP sing 12 n n 
C5' C4' ADP sing 13 n n 
C5' "H5'1" ADP sing 14 n n 
C5' "H5'2" ADP sing 15 n n 
C4' O4' ADP sing 16 n n 
C4' C3' ADP sing 17 n n 
C4' H4' ADP sing 18 n n 
O4' C1' ADP sing 19 n n 
C3' O3' ADP sing 20 n n 
C3' C2' ADP sing 21 n n 
C3' H3' ADP sing 22 n n 
O3' HO3' ADP sing 23 n n 
C2' O2' ADP sing 24 n n 
C2' C1' ADP sing 25 n n 
C2' H2' ADP sing 26 n n 
O2' HO2' ADP sing 27 n n 
C1' N9 ADP sing 28 n n 
C1' H1' ADP sing 29 n n 
N9 C8 ADP sing 30 n y 
N9 C4 ADP sing 31 n y 
C8 N7 ADP doub 32 n y 
C8 H8 ADP sing 33 n n 
N7 C5 ADP sing 34 n y 
C5 C6 ADP sing 35 n y 
C5 C4 ADP doub 36 n y 
C6 N6 ADP sing 37 n n 
C6 N1 ADP doub 38 n y 
N6 HN61 ADP sing 39 n n 
N6 HN62 ADP sing 40 n n 
N1 C2 ADP sing 41 n y 
C2 N3 ADP doub 42 n y 
C2 H2 ADP sing 43 n n 
N3 C4 ADP sing 44 n y 
#
_atom_sites.entry_id                     3C51 
_atom_sites.fract_transf_matrix[1][1]    0.017048 
_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]    0.010808 
_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]    0.003855 
_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 MG A 1 563 563 MG MG . 
D 2 MG A 1 564 564 MG MG . 
E 3 BR A 1 566 566 BR BR . 
F 3 BR A 1 567 1 BR BR . 
G 3 BR A 1 568 2 BR BR . 
H 4 ADP A 1 562 562 ADP ADP . 
I 3 BR B 1 565 565 BR BR . 
J 2 MG B 1 563 563 MG MG . 
K 2 MG B 1 564 564 MG MG . 
L 3 BR B 1 566 565 BR BR . 
M 4 ADP B 1 562 562 ADP ADP . 
#
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 PB ADP . . . M 4 -2.756 -0.508 -102.039 1 133.48 ? PB ADP 562 B 1 
HETATM 2 O O1B ADP . . . M 4 -3.61 -1.465 -102.837 1 134.7 ? O1B ADP 562 B 1 
HETATM 3 O O2B ADP . . . M 4 -2.104 -1.138 -100.832 1 133.75 ? O2B ADP 562 B 1 
HETATM 4 O O3B ADP . . . M 4 -1.845 0.338 -102.893 1 132.03 ? O3B ADP 562 B 1 
HETATM 5 P PA ADP . . . M 4 -3.283 1.917 -100.731 1 135.14 ? PA ADP 562 B 1 
HETATM 6 O O1A ADP . . . M 4 -2.183 1.604 -99.74 1 133.39 ? O1A ADP 562 B 1 
HETATM 7 O O2A ADP . . . M 4 -3.026 2.894 -101.855 1 135.29 ? O2A ADP 562 B 1 
HETATM 8 O O3A ADP . . . M 4 -3.799 0.542 -101.398 1 133.93 ? O3A ADP 562 B 1 
HETATM 9 O O5' ADP . . . M 4 -4.567 2.456 -99.918 1 133.91 ? O5' ADP 562 B 1 
HETATM 10 C C5' ADP . . . M 4 -5.761 2.817 -100.608 1 134.32 ? C5' ADP 562 B 1 
HETATM 11 C C4' ADP . . . M 4 -6.024 4.323 -100.603 1 135.29 ? C4' ADP 562 B 1 
HETATM 12 O O4' ADP . . . M 4 -6.679 4.746 -99.398 1 135.66 ? O4' ADP 562 B 1 
HETATM 13 C C3' ADP . . . M 4 -4.787 5.207 -100.728 1 136.02 ? C3' ADP 562 B 1 
HETATM 14 O O3' ADP . . . M 4 -4.356 5.387 -102.078 1 137.08 ? O3' ADP 562 B 1 
HETATM 15 C C2' ADP . . . M 4 -5.27 6.501 -100.114 1 136.56 ? C2' ADP 562 B 1 
HETATM 16 O O2' ADP . . . M 4 -5.974 7.275 -101.092 1 135.91 ? O2' ADP 562 B 1 
HETATM 17 C C1' ADP . . . M 4 -6.21 6.049 -99.011 1 137.08 ? C1' ADP 562 B 1 
HETATM 18 N N9 ADP . . . M 4 -5.484 5.974 -97.711 1 137.35 ? N9 ADP 562 B 1 
HETATM 19 C C8 ADP . . . M 4 -4.544 5.061 -97.409 1 137.83 ? C8 ADP 562 B 1 
HETATM 20 N N7 ADP . . . M 4 -4.072 5.244 -96.155 1 137.91 ? N7 ADP 562 B 1 
HETATM 21 C C5 ADP . . . M 4 -4.712 6.289 -95.627 1 137.12 ? C5 ADP 562 B 1 
HETATM 22 C C6 ADP . . . M 4 -4.675 7.002 -94.334 1 137.56 ? C6 ADP 562 B 1 
HETATM 23 N N6 ADP . . . M 4 -3.835 6.599 -93.355 1 137.76 ? N6 ADP 562 B 1 
HETATM 24 N N1 ADP . . . M 4 -5.501 8.058 -94.166 1 137.3 ? N1 ADP 562 B 1 
HETATM 25 C C2 ADP . . . M 4 -6.34 8.46 -95.141 1 137.6 ? C2 ADP 562 B 1 
HETATM 26 N N3 ADP . . . M 4 -6.414 7.848 -96.344 1 138.29 ? N3 ADP 562 B 1 
HETATM 27 C C4 ADP . . . M 4 -5.642 6.774 -96.651 1 137.33 ? C4 ADP 562 B 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    32 
_model_server_stats.query_time_ms           334 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           27 
#