data_4DY7
#
_model_server_result.job_id            gJ_cuMvc8Xm38XDE-fabJw 
_model_server_result.datetime_utc      '2024-11-01 01:33:44' 
_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          4dy7 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"J","auth_seq_id":302}' 
#
_entry.id    4DY7 
#
_exptl.entry_id    4DY7 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              22.99 
_entity.id                          6 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'SODIUM ION' 
_entity.pdbx_number_of_molecules    1 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          94.44 
_cell.angle_gamma         90 
_cell.entry_id            4DY7 
_cell.length_a            191.96 
_cell.length_b            86.67 
_cell.length_c            101.89 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4DY7 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 1 2 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 trimeric 3 author_and_software_defined_assembly 1 
PISA trimeric 3 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,B,C,G,H,I,J,K,M,N,O 1 1 
D,E,F,L,P,Q,R 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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      6 
_struct_asym.id                             J 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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 22 A CYS 1 1_555 B SG CYS 119 B CYS 122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf2 B SG CYS 28 B CYS 42 1_555 B SG CYS 44 B CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf3 B SG CYS 173 B CYS 168 1_555 B SG CYS 187 B CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
disulf ? disulf4 B SG CYS 201 B CYS 191 1_555 B SG CYS 231 B CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf5 D SG CYS 22 D CYS 16 1_555 E SG CYS 119 E CYS 122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf6 E SG CYS 28 E CYS 42 1_555 E SG CYS 44 E CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf7 E SG CYS 173 E CYS 168 1_555 E SG CYS 187 E CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf8 E SG CYS 201 E CYS 191 1_555 E SG CYS 231 E CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
metalc ? metalc1 A OD2 ASP 47 A ASP 14 1_555 H CA CA . A CA 102 1_555 L ? ? ? ? ? ? ? ? ? ? ? 2.368 ? 
metalc ? metalc2 A O SER 44 A SER 14 1_555 H CA CA . A CA 102 1_555 I ? ? ? ? ? ? ? ? ? ? ? 2.545 ? 
metalc ? metalc3 A O ARG 49 A ARG 15 1_555 H CA CA . A CA 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.184 ? 
metalc ? metalc4 G OXT ACT . A ACT 101 1_555 H CA CA . A CA 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.348 ? 
metalc ? metalc5 G O ACT . A ACT 101 1_555 H CA CA . A CA 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.828 ? 
metalc ? metalc6 H CA CA . A CA 102 1_555 B O GLY 133 B GLY 133 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.387 ? 
metalc ? metalc7 B O ARG 233 B ARG 221 1_555 J NA NA . B NA 302 1_555 A ? ? ? ? ? ? ? ? ? ? ? 2.646 ? 
metalc ? metalc8 B O LYS 236 B LYS 224 1_555 J NA NA . B NA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.971 ? 
metalc ? metalc9 J NA NA . B NA 302 1_555 N O HOH . B HOH 424 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.134 ? 
metalc ? metalc10 F O THR 309 F THR 309 1_555 L CA CA . F CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.275 ? 
metalc ? metalc11 F O GLY 311 F GLY 311 1_555 L CA CA . F CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.73 ? 
#
_chem_comp.formula           'Na 1' 
_chem_comp.formula_weight    22.99 
_chem_comp.id                NA 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'SODIUM ION' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ? 
#
_atom_sites.entry_id                     4DY7 
_atom_sites.fract_transf_matrix[1][1]    0.005209 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000405 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.011538 
_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]    0.009844 
_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 4 ACT A 1 101 1 ACT ACT . 
H 5 CA A 1 102 1 CA CA . 
I 4 ACT B 1 301 2 ACT ACT . 
J 6 NA B 1 302 2 NA NA . 
K 4 ACT C 1 401 3 ACT ACT . 
L 5 CA F 1 401 3 CA CA . 
M 7 HOH A 1 201 17 HOH HOH . 
M 7 HOH A 2 202 82 HOH HOH . 
N 7 HOH B 1 401 1 HOH HOH . 
N 7 HOH B 2 402 6 HOH HOH . 
N 7 HOH B 3 403 7 HOH HOH . 
N 7 HOH B 4 404 8 HOH HOH . 
N 7 HOH B 5 405 9 HOH HOH . 
N 7 HOH B 6 406 18 HOH HOH . 
N 7 HOH B 7 407 19 HOH HOH . 
N 7 HOH B 8 408 20 HOH HOH . 
N 7 HOH B 9 409 53 HOH HOH . 
N 7 HOH B 10 410 54 HOH HOH . 
N 7 HOH B 11 411 55 HOH HOH . 
N 7 HOH B 12 412 56 HOH HOH . 
N 7 HOH B 13 413 57 HOH HOH . 
N 7 HOH B 14 414 58 HOH HOH . 
N 7 HOH B 15 415 75 HOH HOH . 
N 7 HOH B 16 416 76 HOH HOH . 
N 7 HOH B 17 417 77 HOH HOH . 
N 7 HOH B 18 418 78 HOH HOH . 
N 7 HOH B 19 419 79 HOH HOH . 
N 7 HOH B 20 420 80 HOH HOH . 
N 7 HOH B 21 421 81 HOH HOH . 
N 7 HOH B 22 422 83 HOH HOH . 
N 7 HOH B 23 423 84 HOH HOH . 
N 7 HOH B 24 424 85 HOH HOH . 
N 7 HOH B 25 425 86 HOH HOH . 
O 7 HOH C 1 501 10 HOH HOH . 
O 7 HOH C 2 502 11 HOH HOH . 
O 7 HOH C 3 503 22 HOH HOH . 
O 7 HOH C 4 504 23 HOH HOH . 
O 7 HOH C 5 505 59 HOH HOH . 
O 7 HOH C 6 506 60 HOH HOH . 
O 7 HOH C 7 507 61 HOH HOH . 
O 7 HOH C 8 508 62 HOH HOH . 
O 7 HOH C 9 509 63 HOH HOH . 
O 7 HOH C 10 510 64 HOH HOH . 
O 7 HOH C 11 511 65 HOH HOH . 
O 7 HOH C 12 512 66 HOH HOH . 
O 7 HOH C 13 513 67 HOH HOH . 
O 7 HOH C 14 514 68 HOH HOH . 
O 7 HOH C 15 515 69 HOH HOH . 
O 7 HOH C 16 516 89 HOH HOH . 
O 7 HOH C 17 517 90 HOH HOH . 
O 7 HOH C 18 518 91 HOH HOH . 
O 7 HOH C 19 519 92 HOH HOH . 
O 7 HOH C 20 520 93 HOH HOH . 
O 7 HOH C 21 521 94 HOH HOH . 
O 7 HOH C 22 522 95 HOH HOH . 
O 7 HOH C 23 523 96 HOH HOH . 
O 7 HOH C 24 524 97 HOH HOH . 
O 7 HOH C 25 525 98 HOH HOH . 
O 7 HOH C 26 526 99 HOH HOH . 
P 7 HOH D 1 101 39 HOH HOH . 
P 7 HOH D 2 102 44 HOH HOH . 
P 7 HOH D 3 103 88 HOH HOH . 
Q 7 HOH E 1 401 12 HOH HOH . 
Q 7 HOH E 2 402 24 HOH HOH . 
Q 7 HOH E 3 403 25 HOH HOH . 
Q 7 HOH E 4 404 26 HOH HOH . 
Q 7 HOH E 5 405 37 HOH HOH . 
Q 7 HOH E 6 406 38 HOH HOH . 
Q 7 HOH E 7 407 70 HOH HOH . 
Q 7 HOH E 8 408 87 HOH HOH . 
R 7 HOH F 1 501 2 HOH HOH . 
R 7 HOH F 2 502 3 HOH HOH . 
R 7 HOH F 3 503 4 HOH HOH . 
R 7 HOH F 4 504 5 HOH HOH . 
R 7 HOH F 5 505 13 HOH HOH . 
R 7 HOH F 6 506 14 HOH HOH . 
R 7 HOH F 7 507 15 HOH HOH . 
R 7 HOH F 8 508 16 HOH HOH . 
R 7 HOH F 9 509 27 HOH HOH . 
R 7 HOH F 10 510 28 HOH HOH . 
R 7 HOH F 11 511 29 HOH HOH . 
R 7 HOH F 12 512 30 HOH HOH . 
R 7 HOH F 13 513 31 HOH HOH . 
R 7 HOH F 14 514 32 HOH HOH . 
R 7 HOH F 15 515 33 HOH HOH . 
R 7 HOH F 16 516 34 HOH HOH . 
R 7 HOH F 17 517 35 HOH HOH . 
R 7 HOH F 18 518 36 HOH HOH . 
R 7 HOH F 19 519 40 HOH HOH . 
R 7 HOH F 20 520 41 HOH HOH . 
R 7 HOH F 21 521 42 HOH HOH . 
R 7 HOH F 22 522 43 HOH HOH . 
R 7 HOH F 23 523 45 HOH HOH . 
R 7 HOH F 24 524 46 HOH HOH . 
R 7 HOH F 25 525 47 HOH HOH . 
R 7 HOH F 26 526 48 HOH HOH . 
R 7 HOH F 27 527 49 HOH HOH . 
R 7 HOH F 28 528 50 HOH HOH . 
R 7 HOH F 29 529 51 HOH HOH . 
R 7 HOH F 30 530 52 HOH HOH . 
R 7 HOH F 31 531 71 HOH HOH . 
R 7 HOH F 32 532 72 HOH HOH . 
R 7 HOH F 33 533 73 HOH HOH . 
R 7 HOH F 34 534 74 HOH HOH . 
R 7 HOH F 35 535 100 HOH HOH . 
R 7 HOH F 36 536 101 HOH HOH . 
R 7 HOH F 37 537 102 HOH HOH . 
R 7 HOH F 38 538 103 HOH HOH . 
R 7 HOH F 39 539 104 HOH HOH . 
R 7 HOH F 40 540 105 HOH HOH . 
R 7 HOH F 41 541 106 HOH HOH . 
R 7 HOH F 42 542 107 HOH HOH . 
R 7 HOH F 43 543 108 HOH HOH . 
R 7 HOH F 44 544 109 HOH HOH . 
R 7 HOH F 45 545 110 HOH HOH . 
R 7 HOH F 46 546 111 HOH HOH . 
#
_atom_site.group_PDB             HETATM 
_atom_site.id                    1 
_atom_site.type_symbol           NA 
_atom_site.label_atom_id         NA 
_atom_site.label_comp_id         NA 
_atom_site.label_seq_id          . 
_atom_site.label_alt_id          . 
_atom_site.pdbx_PDB_ins_code     . 
_atom_site.label_asym_id         J 
_atom_site.label_entity_id       6 
_atom_site.Cartn_x               -0.465 
_atom_site.Cartn_y               -21.681 
_atom_site.Cartn_z               -61.414 
_atom_site.occupancy             1 
_atom_site.B_iso_or_equiv        74.69 
_atom_site.pdbx_formal_charge    ? 
_atom_site.auth_atom_id          NA 
_atom_site.auth_comp_id          NA 
_atom_site.auth_seq_id           302 
_atom_site.auth_asym_id          B 
_atom_site.pdbx_PDB_model_num    1 
#
_model_server_stats.io_time_ms              12 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    24 
_model_server_stats.query_time_ms           321 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           1 
#