data_5Z68
#
_model_server_result.job_id            72tcFCI9ak8uRKqz4YGTVQ 
_model_server_result.datetime_utc      '2024-11-09 02:19:39' 
_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          5z68 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"DA","auth_seq_id":405}' 
#
_entry.id    5Z68 
#
_exptl.entry_id    5Z68 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              69.085 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            IMIDAZOLE 
_entity.pdbx_number_of_molecules    21 
_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            5Z68 
_cell.length_a            108.118 
_cell.length_b            138.821 
_cell.length_c            179.567 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5Z68 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
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 dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 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,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,HA,IA 1 1 
C,D,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,JA,KA 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
? 3 F N N 
? 3 G N N 
? 3 H N N 
? 3 I N N 
? 3 J N N 
? 3 K N N 
? 3 N N N 
? 3 O N N 
? 3 P N N 
? 3 Q N N 
? 3 R N N 
? 3 U N N 
? 3 V N N 
? 3 W N N 
? 3 X N N 
? 3 AA N N 
? 3 BA N N 
? 3 CA N N 
? 3 DA N N 
? 3 EA N N 
? 3 FA 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 30 A CYS 22 1_555 A SG CYS 360 A CYS 352 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? 
disulf ? disulf2 B SG CYS 30 B CYS 22 1_555 B SG CYS 360 B CYS 352 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? 
disulf ? disulf3 C SG CYS 30 C CYS 22 1_555 C SG CYS 360 C CYS 352 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? 
disulf ? disulf4 D SG CYS 30 D CYS 22 1_555 D SG CYS 360 D CYS 352 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? 
metalc ? metalc1 A OG SER 45 A SER 37 1_555 L MG MG . A MG 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.905 ? 
metalc ? metalc2 E O2B ATP . A ATP 401 1_555 L MG MG . A MG 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.426 ? 
metalc ? metalc3 L MG MG . A MG 408 1_555 HA O HOH . A HOH 520 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.807 ? 
metalc ? metalc4 B OG SER 45 B SER 37 1_555 S MG MG . B MG 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.176 ? 
metalc ? metalc5 M O3G ATP . B ATP 401 1_555 S MG MG . B MG 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.308 ? 
metalc ? metalc6 M O1B ATP . B ATP 401 1_555 S MG MG . B MG 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.928 ? 
metalc ? metalc7 S MG MG . B MG 407 1_555 IA O HOH . B HOH 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.927 ? 
metalc ? metalc8 S MG MG . B MG 407 1_555 IA O HOH . B HOH 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.887 ? 
metalc ? metalc9 C OG SER 45 C SER 37 1_555 Y MG MG . C MG 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.288 ? 
metalc ? metalc10 T O2G ATP . C ATP 401 1_555 Y MG MG . C MG 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.22 ? 
metalc ? metalc11 T O2B ATP . C ATP 401 1_555 Y MG MG . C MG 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.738 ? 
metalc ? metalc12 T O3A ATP . C ATP 401 1_555 Y MG MG . C MG 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.74 ? 
metalc ? metalc13 Y MG MG . C MG 406 1_555 JA O HOH . C HOH 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.528 ? 
metalc ? metalc14 Y MG MG . C MG 406 1_555 JA O HOH . C HOH 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.772 ? 
metalc ? metalc15 D OG SER 45 D SER 37 1_555 GA MG MG . D MG 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.414 ? 
metalc ? metalc16 Z O1G ATP . D ATP 401 1_555 GA MG MG . D MG 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.947 ? 
metalc ? metalc17 Z O3B ATP . D ATP 401 1_555 GA MG MG . D MG 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.959 ? 
#
_chem_comp.formula           'C3 H5 N2 1' 
_chem_comp.formula_weight    69.085 
_chem_comp.id                IMD 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              IMIDAZOLE 
_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
N1 C2 IMD sing 222 n y 
N1 C5 IMD sing 223 n y 
N1 HN1 IMD sing 224 n n 
C2 N3 IMD doub 225 n y 
C2 H2 IMD sing 226 n n 
N3 C4 IMD sing 227 n y 
N3 HN3 IMD sing 228 n n 
C4 C5 IMD doub 229 n y 
C4 H4 IMD sing 230 n n 
C5 H5 IMD sing 231 n n 
#
_atom_sites.entry_id                     5Z68 
_atom_sites.fract_transf_matrix[1][1]    0.009249 
_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]    0.007204 
_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]    0.005569 
_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
E 2 ATP A 1 401 4 ATP ATP . 
F 3 IMD A 1 402 8 IMD IMD . 
G 3 IMD A 1 403 9 IMD IMD . 
H 3 IMD A 1 404 10 IMD IMD . 
I 3 IMD A 1 405 11 IMD IMD . 
J 3 IMD A 1 406 12 IMD IMD . 
K 3 IMD A 1 407 13 IMD IMD . 
L 4 MG A 1 408 3 MG MG . 
M 2 ATP B 1 401 3 ATP ATP . 
N 3 IMD B 1 402 14 IMD IMD . 
O 3 IMD B 1 403 15 IMD IMD . 
P 3 IMD B 1 404 16 IMD IMD . 
Q 3 IMD B 1 405 17 IMD IMD . 
R 3 IMD B 1 406 18 IMD IMD . 
S 4 MG B 1 407 1 MG MG . 
T 2 ATP C 1 401 1 ATP ATP . 
U 3 IMD C 1 402 5 IMD IMD . 
V 3 IMD C 1 403 6 IMD IMD . 
W 3 IMD C 1 404 19 IMD IMD . 
X 3 IMD C 1 405 21 IMD IMD . 
Y 4 MG C 1 406 2 MG MG . 
Z 2 ATP D 1 401 2 ATP ATP . 
AA 3 IMD D 1 402 1 IMD IMD . 
BA 3 IMD D 1 403 2 IMD IMD . 
CA 3 IMD D 1 404 3 IMD IMD . 
DA 3 IMD D 1 405 4 IMD IMD . 
EA 3 IMD D 1 406 20 IMD IMD . 
FA 3 IMD D 1 407 22 IMD IMD . 
GA 4 MG D 1 408 4 MG MG . 
HA 5 HOH A 1 501 101 HOH HOH . 
HA 5 HOH A 2 502 76 HOH HOH . 
HA 5 HOH A 3 503 79 HOH HOH . 
HA 5 HOH A 4 504 10 HOH HOH . 
HA 5 HOH A 5 505 105 HOH HOH . 
HA 5 HOH A 6 506 92 HOH HOH . 
HA 5 HOH A 7 507 93 HOH HOH . 
HA 5 HOH A 8 508 4 HOH HOH . 
HA 5 HOH A 9 509 11 HOH HOH . 
HA 5 HOH A 10 510 77 HOH HOH . 
HA 5 HOH A 11 511 63 HOH HOH . 
HA 5 HOH A 12 512 75 HOH HOH . 
HA 5 HOH A 13 513 7 HOH HOH . 
HA 5 HOH A 14 514 58 HOH HOH . 
HA 5 HOH A 15 515 3 HOH HOH . 
HA 5 HOH A 16 516 91 HOH HOH . 
HA 5 HOH A 17 517 29 HOH HOH . 
HA 5 HOH A 18 518 88 HOH HOH . 
HA 5 HOH A 19 519 74 HOH HOH . 
HA 5 HOH A 20 520 104 HOH HOH . 
HA 5 HOH A 21 521 8 HOH HOH . 
HA 5 HOH A 22 522 89 HOH HOH . 
HA 5 HOH A 23 523 13 HOH HOH . 
HA 5 HOH A 24 524 78 HOH HOH . 
HA 5 HOH A 25 525 84 HOH HOH . 
HA 5 HOH A 26 526 6 HOH HOH . 
HA 5 HOH A 27 527 61 HOH HOH . 
HA 5 HOH A 28 528 55 HOH HOH . 
HA 5 HOH A 29 529 70 HOH HOH . 
HA 5 HOH A 30 530 60 HOH HOH . 
HA 5 HOH A 31 531 64 HOH HOH . 
HA 5 HOH A 32 532 59 HOH HOH . 
HA 5 HOH A 33 533 65 HOH HOH . 
HA 5 HOH A 34 534 14 HOH HOH . 
HA 5 HOH A 35 535 66 HOH HOH . 
HA 5 HOH A 36 536 94 HOH HOH . 
HA 5 HOH A 37 537 5 HOH HOH . 
HA 5 HOH A 38 538 12 HOH HOH . 
HA 5 HOH A 39 539 90 HOH HOH . 
HA 5 HOH A 40 540 72 HOH HOH . 
IA 5 HOH B 1 501 54 HOH HOH . 
IA 5 HOH B 2 502 53 HOH HOH . 
IA 5 HOH B 3 503 82 HOH HOH . 
IA 5 HOH B 4 504 62 HOH HOH . 
IA 5 HOH B 5 505 95 HOH HOH . 
IA 5 HOH B 6 506 69 HOH HOH . 
IA 5 HOH B 7 507 24 HOH HOH . 
IA 5 HOH B 8 508 9 HOH HOH . 
IA 5 HOH B 9 509 17 HOH HOH . 
IA 5 HOH B 10 510 27 HOH HOH . 
IA 5 HOH B 11 511 22 HOH HOH . 
IA 5 HOH B 12 512 26 HOH HOH . 
IA 5 HOH B 13 513 67 HOH HOH . 
IA 5 HOH B 14 514 32 HOH HOH . 
IA 5 HOH B 15 515 97 HOH HOH . 
IA 5 HOH B 16 516 56 HOH HOH . 
IA 5 HOH B 17 517 68 HOH HOH . 
IA 5 HOH B 18 518 81 HOH HOH . 
IA 5 HOH B 19 519 28 HOH HOH . 
IA 5 HOH B 20 520 57 HOH HOH . 
IA 5 HOH B 21 521 21 HOH HOH . 
IA 5 HOH B 22 522 85 HOH HOH . 
IA 5 HOH B 23 523 25 HOH HOH . 
IA 5 HOH B 24 524 98 HOH HOH . 
IA 5 HOH B 25 525 18 HOH HOH . 
IA 5 HOH B 26 526 20 HOH HOH . 
IA 5 HOH B 27 527 73 HOH HOH . 
IA 5 HOH B 28 528 16 HOH HOH . 
IA 5 HOH B 29 529 31 HOH HOH . 
IA 5 HOH B 30 530 19 HOH HOH . 
IA 5 HOH B 31 531 83 HOH HOH . 
IA 5 HOH B 32 532 30 HOH HOH . 
IA 5 HOH B 33 533 23 HOH HOH . 
IA 5 HOH B 34 534 71 HOH HOH . 
JA 5 HOH C 1 501 2 HOH HOH . 
JA 5 HOH C 2 502 42 HOH HOH . 
JA 5 HOH C 3 503 43 HOH HOH . 
JA 5 HOH C 4 504 86 HOH HOH . 
JA 5 HOH C 5 505 80 HOH HOH . 
JA 5 HOH C 6 506 38 HOH HOH . 
JA 5 HOH C 7 507 39 HOH HOH . 
JA 5 HOH C 8 508 1 HOH HOH . 
JA 5 HOH C 9 509 102 HOH HOH . 
JA 5 HOH C 10 510 96 HOH HOH . 
JA 5 HOH C 11 511 41 HOH HOH . 
JA 5 HOH C 12 512 87 HOH HOH . 
JA 5 HOH C 13 513 40 HOH HOH . 
JA 5 HOH C 14 514 37 HOH HOH . 
JA 5 HOH C 15 515 36 HOH HOH . 
JA 5 HOH C 16 516 107 HOH HOH . 
KA 5 HOH D 1 501 52 HOH HOH . 
KA 5 HOH D 2 502 99 HOH HOH . 
KA 5 HOH D 3 503 50 HOH HOH . 
KA 5 HOH D 4 504 44 HOH HOH . 
KA 5 HOH D 5 505 100 HOH HOH . 
KA 5 HOH D 6 506 49 HOH HOH . 
KA 5 HOH D 7 507 35 HOH HOH . 
KA 5 HOH D 8 508 33 HOH HOH . 
KA 5 HOH D 9 509 103 HOH HOH . 
KA 5 HOH D 10 510 106 HOH HOH . 
KA 5 HOH D 11 511 48 HOH HOH . 
KA 5 HOH D 12 512 47 HOH HOH . 
KA 5 HOH D 13 513 45 HOH HOH . 
KA 5 HOH D 14 514 34 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 N N1 IMD . . . DA 3 24.138 18.99 -63.212 1 82.47 ? N1 IMD 405 D 1 
HETATM 2 C C2 IMD . . . DA 3 24.403 20.309 -63.099 1 91.38 ? C2 IMD 405 D 1 
HETATM 3 N N3 IMD . . . DA 3 23.375 20.912 -62.448 1 96.74 ? N3 IMD 405 D 1 
HETATM 4 C C4 IMD . . . DA 3 22.458 19.961 -62.145 1 99.03 ? C4 IMD 405 D 1 
HETATM 5 C C5 IMD . . . DA 3 22.937 18.747 -62.629 1 86.09 ? C5 IMD 405 D 1 
#
_model_server_stats.io_time_ms              13 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    32 
_model_server_stats.query_time_ms           329 
_model_server_stats.encode_time_ms          9 
_model_server_stats.element_count           5 
#