data_5K7X
#
_model_server_result.job_id            FXTesCIvxxppQLkznWb2Bw 
_model_server_result.datetime_utc      '2024-11-15 14:41:31' 
_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          5k7x 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"CA","auth_seq_id":402}' 
#
_entry.id    5K7X 
#
_exptl.entry_id    5K7X 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              119.076 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            HADACIDIN 
_entity.pdbx_number_of_molecules    6 
_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            5K7X 
_cell.length_a            105.348 
_cell.length_b            130.549 
_cell.length_c            168.673 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5K7X 
_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 
PISA dimeric 2 author_and_software_defined_assembly 3 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,G,H,I,J,K,L,M,N,EA,FA 1 1 
C,D,O,P,Q,R,S,T,U,V,GA,HA 2 1 
E,F,W,X,Y,Z,AA,BA,CA,DA,IA,JA 3 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 I N N 
? 4 M N N 
? 4 Q N N 
? 4 U N N 
? 4 Y N N 
? 4 CA 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 14 A ASP 13 1_555 J MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? 
metalc ? metalc2 A O GLY 43 A GLY 42 1_555 J MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? 
metalc ? metalc3 G O1G GTP . A GTP 400 1_555 J MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.229 ? 
metalc ? metalc4 G O3B GTP . A GTP 400 1_555 J MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.321 ? 
metalc ? metalc5 G O2A GTP . A GTP 400 1_555 J MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.853 ? 
metalc ? metalc6 I O HDA . A HDA 402 1_555 J MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.435 ? 
metalc ? metalc7 B OD1 ASP 14 B ASP 13 1_555 N MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.118 ? 
metalc ? metalc8 B O GLY 43 B GLY 42 1_555 N MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? 
metalc ? metalc9 K O1G GTP . B GTP 400 1_555 N MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.34 ? 
metalc ? metalc10 K O3B GTP . B GTP 400 1_555 N MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.286 ? 
metalc ? metalc11 K O2A GTP . B GTP 400 1_555 N MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.696 ? 
metalc ? metalc12 M O HDA . B HDA 402 1_555 N MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.41 ? 
metalc ? metalc13 C OD1 ASP 14 C ASP 13 1_555 R MG MG . C MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.276 ? 
metalc ? metalc14 C O GLY 43 C GLY 42 1_555 R MG MG . C MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.148 ? 
metalc ? metalc15 O O1G GTP . C GTP 400 1_555 R MG MG . C MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.303 ? 
metalc ? metalc16 O O3B GTP . C GTP 400 1_555 R MG MG . C MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.22 ? 
metalc ? metalc17 O O2A GTP . C GTP 400 1_555 R MG MG . C MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.689 ? 
metalc ? metalc18 Q O HDA . C HDA 402 1_555 R MG MG . C MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.203 ? 
metalc ? metalc19 D OD1 ASP 14 D ASP 13 1_555 V MG MG . D MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.217 ? 
metalc ? metalc20 D O GLY 43 D GLY 42 1_555 V MG MG . D MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.138 ? 
metalc ? metalc21 S O1G GTP . D GTP 400 1_555 V MG MG . D MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.384 ? 
metalc ? metalc22 S O3B GTP . D GTP 400 1_555 V MG MG . D MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.297 ? 
metalc ? metalc23 S O2A GTP . D GTP 400 1_555 V MG MG . D MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.713 ? 
metalc ? metalc24 U O HDA . D HDA 402 1_555 V MG MG . D MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.001 ? 
metalc ? metalc25 E OD1 ASP 14 E ASP 13 1_555 Z MG MG . E MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.176 ? 
metalc ? metalc26 E O GLY 43 E GLY 42 1_555 Z MG MG . E MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.101 ? 
metalc ? metalc27 W O1G GTP . E GTP 400 1_555 Z MG MG . E MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.257 ? 
metalc ? metalc28 W O3B GTP . E GTP 400 1_555 Z MG MG . E MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.264 ? 
metalc ? metalc29 W O2A GTP . E GTP 400 1_555 Z MG MG . E MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.755 ? 
metalc ? metalc30 Y O HDA . E HDA 402 1_555 Z MG MG . E MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.226 ? 
metalc ? metalc31 F OD1 ASP 14 F ASP 13 1_555 DA MG MG . F MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.257 ? 
metalc ? metalc32 F O GLY 43 F GLY 42 1_555 DA MG MG . F MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.152 ? 
metalc ? metalc33 AA O1G GTP . F GTP 400 1_555 DA MG MG . F MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.312 ? 
metalc ? metalc34 AA O3B GTP . F GTP 400 1_555 DA MG MG . F MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.27 ? 
metalc ? metalc35 AA O2A GTP . F GTP 400 1_555 DA MG MG . F MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.858 ? 
metalc ? metalc36 CA O HDA . F HDA 402 1_555 DA MG MG . F MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.375 ? 
#
_chem_comp.formula           'C3 H5 N O4' 
_chem_comp.formula_weight    119.076 
_chem_comp.id                HDA 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              HADACIDIN 
_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
NA C HDA sing 179 n n 
NA OB HDA sing 180 n n 
NA CB HDA sing 181 n n 
C O HDA doub 182 n n 
C HC HDA sing 183 n n 
OB HOB HDA sing 184 n n 
CB CG HDA sing 185 n n 
CB HB1 HDA sing 186 n n 
CB HB2 HDA sing 187 n n 
CG OD1 HDA doub 188 n n 
CG OD2 HDA sing 189 n n 
OD2 HOD HDA sing 190 n n 
#
_atom_sites.entry_id                     5K7X 
_atom_sites.fract_transf_matrix[1][1]    0.009492 
_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]    0.00766 
_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]    0.005929 
_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 GTP A 1 400 400 GTP GTP . 
H 3 IMP A 1 401 401 IMP IMP . 
I 4 HDA A 1 402 402 HDA HDA . 
J 5 MG A 1 403 403 MG MG . 
K 2 GTP B 1 400 400 GTP GTP . 
L 3 IMP B 1 401 401 IMP IMP . 
M 4 HDA B 1 402 402 HDA HDA . 
N 5 MG B 1 403 403 MG MG . 
O 2 GTP C 1 400 400 GTP GTP . 
P 3 IMP C 1 401 401 IMP IMP . 
Q 4 HDA C 1 402 402 HDA HDA . 
R 5 MG C 1 403 403 MG MG . 
S 2 GTP D 1 400 400 GTP GTP . 
T 3 IMP D 1 401 401 IMP IMP . 
U 4 HDA D 1 402 402 HDA HDA . 
V 5 MG D 1 403 403 MG MG . 
W 2 GTP E 1 400 400 GTP GTP . 
X 3 IMP E 1 401 401 IMP IMP . 
Y 4 HDA E 1 402 402 HDA HDA . 
Z 5 MG E 1 403 403 MG MG . 
AA 2 GTP F 1 400 400 GTP GTP . 
BA 3 IMP F 1 401 401 IMP IMP . 
CA 4 HDA F 1 402 402 HDA HDA . 
DA 5 MG F 1 403 403 MG MG . 
EA 6 HOH A 1 501 6 HOH HOH . 
EA 6 HOH A 2 502 55 HOH HOH . 
EA 6 HOH A 3 503 19 HOH HOH . 
EA 6 HOH A 4 504 2 HOH HOH . 
EA 6 HOH A 5 505 4 HOH HOH . 
EA 6 HOH A 6 506 53 HOH HOH . 
EA 6 HOH A 7 507 1 HOH HOH . 
EA 6 HOH A 8 508 58 HOH HOH . 
EA 6 HOH A 9 509 29 HOH HOH . 
EA 6 HOH A 10 510 52 HOH HOH . 
FA 6 HOH B 1 501 28 HOH HOH . 
FA 6 HOH B 2 502 47 HOH HOH . 
FA 6 HOH B 3 503 35 HOH HOH . 
FA 6 HOH B 4 504 57 HOH HOH . 
FA 6 HOH B 5 505 32 HOH HOH . 
FA 6 HOH B 6 506 10 HOH HOH . 
FA 6 HOH B 7 507 22 HOH HOH . 
FA 6 HOH B 8 508 39 HOH HOH . 
FA 6 HOH B 9 509 33 HOH HOH . 
FA 6 HOH B 10 510 54 HOH HOH . 
FA 6 HOH B 11 511 20 HOH HOH . 
FA 6 HOH B 12 512 51 HOH HOH . 
FA 6 HOH B 13 513 48 HOH HOH . 
GA 6 HOH C 1 501 25 HOH HOH . 
GA 6 HOH C 2 502 12 HOH HOH . 
GA 6 HOH C 3 503 7 HOH HOH . 
GA 6 HOH C 4 504 37 HOH HOH . 
GA 6 HOH C 5 505 41 HOH HOH . 
GA 6 HOH C 6 506 17 HOH HOH . 
GA 6 HOH C 7 507 46 HOH HOH . 
GA 6 HOH C 8 508 11 HOH HOH . 
GA 6 HOH C 9 509 56 HOH HOH . 
GA 6 HOH C 10 510 18 HOH HOH . 
GA 6 HOH C 11 511 13 HOH HOH . 
GA 6 HOH C 12 512 26 HOH HOH . 
HA 6 HOH D 1 501 31 HOH HOH . 
HA 6 HOH D 2 502 45 HOH HOH . 
HA 6 HOH D 3 503 9 HOH HOH . 
HA 6 HOH D 4 504 16 HOH HOH . 
HA 6 HOH D 5 505 43 HOH HOH . 
IA 6 HOH E 1 501 34 HOH HOH . 
IA 6 HOH E 2 502 44 HOH HOH . 
IA 6 HOH E 3 503 42 HOH HOH . 
IA 6 HOH E 4 504 49 HOH HOH . 
IA 6 HOH E 5 505 30 HOH HOH . 
IA 6 HOH E 6 506 38 HOH HOH . 
JA 6 HOH F 1 501 50 HOH HOH . 
JA 6 HOH F 2 502 15 HOH HOH . 
JA 6 HOH F 3 503 40 HOH HOH . 
JA 6 HOH F 4 504 36 HOH HOH . 
JA 6 HOH F 5 505 21 HOH HOH . 
JA 6 HOH F 6 506 24 HOH HOH . 
JA 6 HOH F 7 507 14 HOH HOH . 
JA 6 HOH F 8 508 27 HOH HOH . 
JA 6 HOH F 9 509 5 HOH HOH . 
JA 6 HOH F 10 510 3 HOH HOH . 
JA 6 HOH F 11 511 23 HOH HOH . 
JA 6 HOH F 12 512 8 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 NA HDA . . . CA 4 13.848 4.298 23.172 1 76.21 ? NA HDA 402 F 1 
HETATM 2 C C HDA . . . CA 4 14.103 4.567 21.995 1 75.68 ? C HDA 402 F 1 
HETATM 3 O O HDA . . . CA 4 14.041 3.635 21.232 1 74.65 ? O HDA 402 F 1 
HETATM 4 O OB HDA . . . CA 4 13.189 3.096 23.392 1 73.97 ? OB HDA 402 F 1 
HETATM 5 C CB HDA . . . CA 4 14.22 5.193 24.254 1 58.37 ? CB HDA 402 F 1 
HETATM 6 C CG HDA . . . CA 4 15.141 4.42 25.113 1 50.26 ? CG HDA 402 F 1 
HETATM 7 O OD1 HDA . . . CA 4 16.16 3.998 24.611 1 50.01 ? OD1 HDA 402 F 1 
HETATM 8 O OD2 HDA . . . CA 4 14.875 4.185 26.275 1 62.43 ? OD2 HDA 402 F 1 
#
_model_server_stats.io_time_ms              32 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    20 
_model_server_stats.query_time_ms           265 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           8 
#