data_6D5K
#
_model_server_result.job_id            1khaT_SAqc1e-tJ28JaSog 
_model_server_result.datetime_utc      '2024-11-01 01:08:06' 
_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          6d5k 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"N","auth_seq_id":303}' 
#
_entry.id    6D5K 
#
_exptl.entry_id    6D5K 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              238.305 
_entity.id                          7 
_entity.src_method                  man 
_entity.type                        non-polymer 
_entity.pdbx_description            '4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID' 
_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          90 
_cell.angle_gamma         120 
_cell.entry_id            6D5K 
_cell.length_a            112.252 
_cell.length_b            112.252 
_cell.length_c            117.993 
_cell.Z_PDB               18 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6D5K 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        152 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 31 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 hexameric 6 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,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T 1 1 
A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T 2 1,2 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 6_554 -x,-x+y,-z-2/3 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 0 0 -78.662 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      7 
_struct_asym.id                             N 
_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
metalc ? metalc1 D C5' 5AD . A 5AD 301 1_555 E CO B12 . A B12 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? 
metalc ? metalc2 F CO B12 . A B12 303 1_555 I C5' 5AD . B 5AD 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.007 ? 
metalc ? metalc3 C OD1 ASN 160 C ASN 214 1_555 Q MG MG . C MG 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.998 ? 
metalc ? metalc4 L O1A ATP . C ATP 301 1_555 M MG MG . C MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.679 ? 
metalc ? metalc5 L O3G ATP . C ATP 301 1_555 Q MG MG . C MG 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.986 ? 
metalc ? metalc6 L O2B ATP . C ATP 301 1_555 Q MG MG . C MG 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.837 ? 
metalc ? metalc7 L O2A ATP . C ATP 301 1_555 Q MG MG . C MG 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.884 ? 
metalc ? metalc8 M MG MG . C MG 302 1_555 T O HOH . C HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.196 ? 
metalc ? metalc9 M MG MG . C MG 302 1_555 T O HOH . C HOH 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.578 ? 
metalc ? metalc10 M MG MG . C MG 302 1_555 T O HOH . C HOH 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.167 ? 
metalc ? metalc11 M MG MG . C MG 302 1_555 T O HOH . C HOH 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? 
metalc ? metalc12 Q MG MG . C MG 306 1_555 T O HOH . C HOH 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.867 ? 
metalc ? metalc13 Q MG MG . C MG 306 1_555 T O HOH . C HOH 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.076 ? 
#
_chem_comp.formula           'C8 H18 N2 O4 S' 
_chem_comp.formula_weight    238.305 
_chem_comp.id                EPE 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     HEPES 
#
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 EPE sing 355 n n 
N1 C6 EPE sing 356 n n 
N1 C9 EPE sing 357 n n 
C2 C3 EPE sing 358 n n 
C2 H21 EPE sing 359 n n 
C2 H22 EPE sing 360 n n 
C3 N4 EPE sing 361 n n 
C3 H31 EPE sing 362 n n 
C3 H32 EPE sing 363 n n 
N4 C5 EPE sing 364 n n 
N4 C7 EPE sing 365 n n 
C5 C6 EPE sing 366 n n 
C5 H51 EPE sing 367 n n 
C5 H52 EPE sing 368 n n 
C6 H61 EPE sing 369 n n 
C6 H62 EPE sing 370 n n 
C7 C8 EPE sing 371 n n 
C7 H71 EPE sing 372 n n 
C7 H72 EPE sing 373 n n 
C8 O8 EPE sing 374 n n 
C8 H81 EPE sing 375 n n 
C8 H82 EPE sing 376 n n 
O8 HO8 EPE sing 377 n n 
C9 C10 EPE sing 378 n n 
C9 H91 EPE sing 379 n n 
C9 H92 EPE sing 380 n n 
C10 S EPE sing 381 n n 
C10 H101 EPE sing 382 n n 
C10 H102 EPE sing 383 n n 
S O1S EPE doub 384 n n 
S O2S EPE doub 385 n n 
S O3S EPE sing 386 n n 
O3S HOS3 EPE sing 387 n n 
#
_atom_sites.entry_id                     6D5K 
_atom_sites.fract_transf_matrix[1][1]    0.008909 
_atom_sites.fract_transf_matrix[1][2]    0.005143 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.010287 
_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]    0.008475 
_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
D 2 5AD A 1 301 1 5AD 5AD . 
E 3 B12 A 1 302 2 B12 B12 . 
F 3 B12 A 1 303 4 B12 B12 . 
G 4 SO4 A 1 304 3 SO4 SO4 . 
H 4 SO4 A 1 305 6 SO4 SO4 . 
I 2 5AD B 1 301 3 5AD 5AD . 
J 4 SO4 B 1 302 1 SO4 SO4 . 
K 4 SO4 B 1 303 5 SO4 SO4 . 
L 5 ATP C 1 301 1 ATP ATP . 
M 6 MG C 1 302 1 MG MG . 
N 7 EPE C 1 303 1 EPE EPE . 
O 4 SO4 C 1 304 2 SO4 SO4 . 
P 4 SO4 C 1 305 4 SO4 SO4 . 
Q 6 MG C 1 306 2 MG MG . 
R 8 HOH A 1 401 7 HOH HOH . 
R 8 HOH A 2 402 64 HOH HOH . 
R 8 HOH A 3 403 58 HOH HOH . 
R 8 HOH A 4 404 70 HOH HOH . 
S 8 HOH B 1 401 71 HOH HOH . 
S 8 HOH B 2 402 54 HOH HOH . 
S 8 HOH B 3 403 19 HOH HOH . 
S 8 HOH B 4 404 63 HOH HOH . 
S 8 HOH B 5 405 44 HOH HOH . 
S 8 HOH B 6 406 40 HOH HOH . 
T 8 HOH C 1 401 1 HOH HOH . 
T 8 HOH C 2 402 5 HOH HOH . 
T 8 HOH C 3 403 2 HOH HOH . 
T 8 HOH C 4 404 3 HOH HOH . 
T 8 HOH C 5 405 6 HOH HOH . 
T 8 HOH C 6 406 16 HOH HOH . 
T 8 HOH C 7 407 4 HOH HOH . 
T 8 HOH C 8 408 13 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 EPE . . . N 7 -19.005 57.904 -15.191 1 132.51 ? N1 EPE 303 C 1 
HETATM 2 C C2 EPE . . . N 7 -17.827 58.758 -14.948 1 126.48 ? C2 EPE 303 C 1 
HETATM 3 C C3 EPE . . . N 7 -17.177 59.125 -16.279 1 124.75 ? C3 EPE 303 C 1 
HETATM 4 N N4 EPE . . . N 7 -17.063 57.998 -17.193 1 114.97 ? N4 EPE 303 C 1 
HETATM 5 C C5 EPE . . . N 7 -17.432 56.674 -16.739 1 116.09 ? C5 EPE 303 C 1 
HETATM 6 C C6 EPE . . . N 7 -18.644 56.614 -15.814 1 122.49 ? C6 EPE 303 C 1 
HETATM 7 C C7 EPE . . . N 7 -16.027 58.042 -18.2 1 106.97 ? C7 EPE 303 C 1 
HETATM 8 C C8 EPE . . . N 7 -14.869 57.11 -17.858 1 106.24 ? C8 EPE 303 C 1 
HETATM 9 O O8 EPE . . . N 7 -14.205 56.682 -19.027 1 113.22 ? O8 EPE 303 C 1 
HETATM 10 C C9 EPE . . . N 7 -19.744 57.647 -13.933 1 133.1 ? C9 EPE 303 C 1 
HETATM 11 C C10 EPE . . . N 7 -19.001 56.649 -13.038 1 140.24 ? C10 EPE 303 C 1 
HETATM 12 S S EPE . . . N 7 -19.807 55.029 -12.812 1 151.09 ? S EPE 303 C 1 
HETATM 13 O O1S EPE . . . N 7 -18.815 53.959 -12.915 1 129.79 ? O1S EPE 303 C 1 
HETATM 14 O O2S EPE . . . N 7 -20.815 54.813 -13.839 1 137.73 ? O2S EPE 303 C 1 
HETATM 15 O O3S EPE . . . N 7 -20.46 54.973 -11.502 1 136.11 ? O3S EPE 303 C 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           327 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           15 
#