data_3DVL
#
_model_server_result.job_id            JiJmN9khps220GGjQaj16g 
_model_server_result.datetime_utc      '2024-11-14 18:07:08' 
_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          3dvl 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"T","auth_seq_id":901}' 
#
_entry.id    3DVL 
#
_exptl.entry_id    3DVL 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              507.181 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "ADENOSINE-5'-TRIPHOSPHATE" 
_entity.pdbx_number_of_molecules    12 
_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            3DVL 
_cell.length_a            132.873 
_cell.length_b            135.576 
_cell.length_c            204.951 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3DVL 
_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    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,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA 
_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 H N N 
? 3 I N N 
? 3 K N N 
? 3 L N N 
? 3 N N N 
? 3 O N N 
? 3 Q N N 
? 3 R N N 
? 3 T N N 
? 3 U N N 
? 3 W N N 
? 3 X 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
covale ? covale1 A C ILE 430 A ILE 430 1_555 A N SEP 431 A SEP 431 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? 
covale ? covale2 A C SEP 431 A SEP 431 1_555 A N TPO 432 A TPO 432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.321 ? 
covale ? covale3 A C TPO 432 A TPO 432 1_555 A N ILE 433 A ILE 433 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? 
covale ? covale4 B C ILE 430 B ILE 430 1_555 B N SEP 431 B SEP 431 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? 
covale ? covale5 B C SEP 431 B SEP 431 1_555 B N TPO 432 B TPO 432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? 
covale ? covale6 B C TPO 432 B TPO 432 1_555 B N ILE 433 B ILE 433 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? 
covale ? covale7 C C ILE 430 C ILE 430 1_555 C N SEP 431 C SEP 431 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? 
covale ? covale8 C C SEP 431 C SEP 431 1_555 C N TPO 432 C TPO 432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? 
covale ? covale9 C C TPO 432 C TPO 432 1_555 C N ILE 433 C ILE 433 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? 
covale ? covale10 D C ILE 430 D ILE 430 1_555 D N SEP 431 D SEP 431 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? 
covale ? covale11 D C SEP 431 D SEP 431 1_555 D N TPO 432 D TPO 432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? 
covale ? covale12 D C TPO 432 D TPO 432 1_555 D N ILE 433 D ILE 433 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? 
covale ? covale13 E C ILE 430 E ILE 430 1_555 E N SEP 431 E SEP 431 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? 
covale ? covale14 E C SEP 431 E SEP 431 1_555 E N TPO 432 E TPO 432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? 
covale ? covale15 E C TPO 432 E TPO 432 1_555 E N ILE 433 E ILE 433 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.317 ? 
covale ? covale16 F C ILE 430 F ILE 430 1_555 F N SEP 431 F SEP 431 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? 
covale ? covale17 F C SEP 431 F SEP 431 1_555 F N TPO 432 F TPO 432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.311 ? 
covale ? covale18 F C TPO 432 F TPO 432 1_555 F N ILE 433 F ILE 433 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.245 ? 
metalc ? metalc1 B OE1 GLU 318 B GLU 318 1_555 J MG MG . B MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.367 ? 
metalc ? metalc2 C OG1 THR 295 C THR 295 1_555 M MG MG . C MG 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.257 ? 
metalc ? metalc3 D OG1 THR 295 D THR 295 1_555 P MG MG . D MG 804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.945 ? 
metalc ? metalc4 E OG1 THR 295 E THR 295 1_555 S MG MG . E MG 805 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.134 ? 
#
_chem_comp.formula           'C10 H16 N5 O13 P3' 
_chem_comp.formula_weight    507.181 
_chem_comp.id                ATP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "ADENOSINE-5'-TRIPHOSPHATE" 
_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 ATP doub 70 n n 
PG O2G ATP sing 71 n n 
PG O3G ATP sing 72 n n 
PG O3B ATP sing 73 n n 
O2G HOG2 ATP sing 74 n n 
O3G HOG3 ATP sing 75 n n 
PB O1B ATP doub 76 n n 
PB O2B ATP sing 77 n n 
PB O3B ATP sing 78 n n 
PB O3A ATP sing 79 n n 
O2B HOB2 ATP sing 80 n n 
PA O1A ATP doub 81 n n 
PA O2A ATP sing 82 n n 
PA O3A ATP sing 83 n n 
PA O5' ATP sing 84 n n 
O2A HOA2 ATP sing 85 n n 
O5' C5' ATP sing 86 n n 
C5' C4' ATP sing 87 n n 
C5' "H5'1" ATP sing 88 n n 
C5' "H5'2" ATP sing 89 n n 
C4' O4' ATP sing 90 n n 
C4' C3' ATP sing 91 n n 
C4' H4' ATP sing 92 n n 
O4' C1' ATP sing 93 n n 
C3' O3' ATP sing 94 n n 
C3' C2' ATP sing 95 n n 
C3' H3' ATP sing 96 n n 
O3' HO3' ATP sing 97 n n 
C2' O2' ATP sing 98 n n 
C2' C1' ATP sing 99 n n 
C2' H2' ATP sing 100 n n 
O2' HO2' ATP sing 101 n n 
C1' N9 ATP sing 102 n n 
C1' H1' ATP sing 103 n n 
N9 C8 ATP sing 104 n y 
N9 C4 ATP sing 105 n y 
C8 N7 ATP doub 106 n y 
C8 H8 ATP sing 107 n n 
N7 C5 ATP sing 108 n y 
C5 C6 ATP sing 109 n y 
C5 C4 ATP doub 110 n y 
C6 N6 ATP sing 111 n n 
C6 N1 ATP doub 112 n y 
N6 HN61 ATP sing 113 n n 
N6 HN62 ATP sing 114 n n 
N1 C2 ATP sing 115 n y 
C2 N3 ATP doub 116 n y 
C2 H2 ATP sing 117 n n 
N3 C4 ATP sing 118 n y 
#
_atom_sites.entry_id                     3DVL 
_atom_sites.fract_transf_matrix[1][1]    0.007526 
_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]    0.007376 
_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]    0.004879 
_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
G 2 MG A 1 801 801 MG MG . 
H 3 ATP A 1 901 901 ATP ATP . 
I 3 ATP A 1 903 903 ATP ATP . 
J 2 MG B 1 802 802 MG MG . 
K 3 ATP B 1 901 901 ATP ATP . 
L 3 ATP B 1 903 903 ATP ATP . 
M 2 MG C 1 803 803 MG MG . 
N 3 ATP C 1 901 901 ATP ATP . 
O 3 ATP C 1 903 903 ATP ATP . 
P 2 MG D 1 804 804 MG MG . 
Q 3 ATP D 1 901 901 ATP ATP . 
R 3 ATP D 1 903 903 ATP ATP . 
S 2 MG E 1 805 805 MG MG . 
T 3 ATP E 1 901 901 ATP ATP . 
U 3 ATP E 1 903 903 ATP ATP . 
V 2 MG F 1 806 806 MG MG . 
W 3 ATP F 1 901 901 ATP ATP . 
X 3 ATP F 1 903 903 ATP ATP . 
Y 4 HOH A 1 520 4 HOH HOH . 
Y 4 HOH A 2 521 8 HOH HOH . 
Y 4 HOH A 3 522 11 HOH HOH . 
Y 4 HOH A 4 523 23 HOH HOH . 
Y 4 HOH A 5 524 30 HOH HOH . 
Y 4 HOH A 6 525 45 HOH HOH . 
Y 4 HOH A 7 526 63 HOH HOH . 
Z 4 HOH B 1 520 17 HOH HOH . 
Z 4 HOH B 2 521 21 HOH HOH . 
Z 4 HOH B 3 522 37 HOH HOH . 
Z 4 HOH B 4 523 38 HOH HOH . 
Z 4 HOH B 5 524 61 HOH HOH . 
AA 4 HOH C 1 520 16 HOH HOH . 
AA 4 HOH C 2 521 18 HOH HOH . 
AA 4 HOH C 3 522 32 HOH HOH . 
AA 4 HOH C 4 523 39 HOH HOH . 
AA 4 HOH C 5 524 43 HOH HOH . 
AA 4 HOH C 6 525 44 HOH HOH . 
AA 4 HOH C 7 526 46 HOH HOH . 
BA 4 HOH D 1 520 5 HOH HOH . 
BA 4 HOH D 2 521 7 HOH HOH . 
BA 4 HOH D 3 522 10 HOH HOH . 
BA 4 HOH D 4 523 12 HOH HOH . 
BA 4 HOH D 5 524 24 HOH HOH . 
BA 4 HOH D 6 525 29 HOH HOH . 
BA 4 HOH D 7 526 53 HOH HOH . 
BA 4 HOH D 8 527 57 HOH HOH . 
BA 4 HOH D 9 528 60 HOH HOH . 
BA 4 HOH D 10 529 64 HOH HOH . 
BA 4 HOH D 11 530 65 HOH HOH . 
BA 4 HOH D 12 531 72 HOH HOH . 
CA 4 HOH E 1 520 2 HOH HOH . 
CA 4 HOH E 2 521 3 HOH HOH . 
CA 4 HOH E 3 522 9 HOH HOH . 
CA 4 HOH E 4 523 19 HOH HOH . 
CA 4 HOH E 5 524 20 HOH HOH . 
CA 4 HOH E 6 525 36 HOH HOH . 
CA 4 HOH E 7 526 41 HOH HOH . 
CA 4 HOH E 8 527 51 HOH HOH . 
CA 4 HOH E 9 528 69 HOH HOH . 
CA 4 HOH E 10 529 73 HOH HOH . 
DA 4 HOH F 1 520 1 HOH HOH . 
DA 4 HOH F 2 521 6 HOH HOH . 
DA 4 HOH F 3 522 13 HOH HOH . 
DA 4 HOH F 4 523 14 HOH HOH . 
DA 4 HOH F 5 524 15 HOH HOH . 
DA 4 HOH F 6 525 22 HOH HOH . 
DA 4 HOH F 7 526 27 HOH HOH . 
DA 4 HOH F 8 527 31 HOH HOH . 
DA 4 HOH F 9 528 33 HOH HOH . 
DA 4 HOH F 10 529 35 HOH HOH . 
DA 4 HOH F 11 530 48 HOH HOH . 
DA 4 HOH F 12 531 49 HOH HOH . 
DA 4 HOH F 13 532 52 HOH HOH . 
DA 4 HOH F 14 533 54 HOH HOH . 
DA 4 HOH F 15 534 56 HOH HOH . 
DA 4 HOH F 16 535 58 HOH HOH . 
DA 4 HOH F 17 536 59 HOH HOH . 
DA 4 HOH F 18 537 62 HOH HOH . 
DA 4 HOH F 19 538 66 HOH HOH . 
DA 4 HOH F 20 539 67 HOH HOH . 
DA 4 HOH F 21 540 68 HOH HOH . 
DA 4 HOH F 22 541 70 HOH HOH . 
DA 4 HOH F 23 542 71 HOH HOH . 
DA 4 HOH F 24 543 74 HOH HOH . 
DA 4 HOH F 25 544 78 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 ATP . . . T 3 83.05 94.147 19.338 1 104.54 ? PG ATP 901 E 1 
HETATM 2 O O1G ATP . . . T 3 84.374 94.037 18.718 1 100.43 ? O1G ATP 901 E 1 
HETATM 3 O O2G ATP . . . T 3 83.066 93.513 20.754 1 113.06 ? O2G ATP 901 E 1 
HETATM 4 O O3G ATP . . . T 3 82.651 95.63 19.385 1 99.7 ? O3G ATP 901 E 1 
HETATM 5 P PB ATP . . . T 3 81.37 93.794 17.054 1 66.46 ? PB ATP 901 E 1 
HETATM 6 O O1B ATP . . . T 3 80.562 92.71 16.637 1 66.54 ? O1B ATP 901 E 1 
HETATM 7 O O2B ATP . . . T 3 82.374 94.199 16.025 1 79.4 ? O2B ATP 901 E 1 
HETATM 8 O O3B ATP . . . T 3 81.984 93.362 18.407 1 87.95 ? O3B ATP 901 E 1 
HETATM 9 P PA ATP . . . T 3 79.989 96.348 16.744 1 68.38 ? PA ATP 901 E 1 
HETATM 10 O O1A ATP . . . T 3 79.105 96.197 15.622 1 61.27 ? O1A ATP 901 E 1 
HETATM 11 O O2A ATP . . . T 3 79.405 97.15 17.902 1 69.99 ? O2A ATP 901 E 1 
HETATM 12 O O3A ATP . . . T 3 80.303 94.895 17.326 1 72.81 ? O3A ATP 901 E 1 
HETATM 13 O O5' ATP . . . T 3 81.301 97.067 16.204 1 69.14 ? O5' ATP 901 E 1 
HETATM 14 C C5' ATP . . . T 3 81.411 98.53 16.318 1 70.02 ? C5' ATP 901 E 1 
HETATM 15 C C4' ATP . . . T 3 82.119 99.165 15.094 1 72.08 ? C4' ATP 901 E 1 
HETATM 16 O O4' ATP . . . T 3 81.218 99.806 14.233 1 69.36 ? O4' ATP 901 E 1 
HETATM 17 C C3' ATP . . . T 3 83.202 100.179 15.422 1 70.27 ? C3' ATP 901 E 1 
HETATM 18 O O3' ATP . . . T 3 84.468 99.519 15.392 1 76.88 ? O3' ATP 901 E 1 
HETATM 19 C C2' ATP . . . T 3 83.055 101.265 14.375 1 71.95 ? C2' ATP 901 E 1 
HETATM 20 O O2' ATP . . . T 3 83.946 101.294 13.313 1 78.34 ? O2' ATP 901 E 1 
HETATM 21 C C1' ATP . . . T 3 81.658 101.108 13.881 1 72.76 ? C1' ATP 901 E 1 
HETATM 22 N N9 ATP . . . T 3 80.602 102.069 14.362 1 76.21 ? N9 ATP 901 E 1 
HETATM 23 C C8 ATP . . . T 3 79.882 101.992 15.541 1 77.25 ? C8 ATP 901 E 1 
HETATM 24 N N7 ATP . . . T 3 79.088 103.038 15.573 1 77.1 ? N7 ATP 901 E 1 
HETATM 25 C C5 ATP . . . T 3 79.248 103.819 14.455 1 79.05 ? C5 ATP 901 E 1 
HETATM 26 C C6 ATP . . . T 3 78.721 105.034 13.927 1 80.38 ? C6 ATP 901 E 1 
HETATM 27 N N6 ATP . . . T 3 77.855 105.804 14.51 1 78.05 ? N6 ATP 901 E 1 
HETATM 28 N N1 ATP . . . T 3 79.155 105.525 12.698 1 80.4 ? N1 ATP 901 E 1 
HETATM 29 C C2 ATP . . . T 3 80.113 104.865 11.971 1 83.27 ? C2 ATP 901 E 1 
HETATM 30 N N3 ATP . . . T 3 80.66 103.682 12.46 1 84.21 ? N3 ATP 901 E 1 
HETATM 31 C C4 ATP . . . T 3 80.224 103.183 13.689 1 78.55 ? C4 ATP 901 E 1 
#
_model_server_stats.io_time_ms              14 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    50 
_model_server_stats.query_time_ms           311 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           31 
#