data_5KND
#
_model_server_result.job_id            7zJAwOSnYObzCgPJ8VSajg 
_model_server_result.datetime_utc      '2025-02-02 18:06:57' 
_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          5knd 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"M","auth_seq_id":502}' 
#
_entry.id    5KND 
#
_exptl.entry_id    5KND 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              282.334 
_entity.id                          8 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL 
_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         90 
_cell.entry_id            5KND 
_cell.length_a            128.22 
_cell.length_b            128.352 
_cell.length_c            228.033 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5KND 
_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    octameric 
_pdbx_struct_assembly.oligomeric_count      8 
_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 
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      8 
_struct_asym.id                             M 
_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 C OG1 THR 246 C THR 239 1_555 I MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.971 ? 
metalc ? metalc2 I MG MG . C MG 601 1_555 K O4 PO4 . C PO4 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? 
metalc ? metalc3 I MG MG . C MG 601 1_555 Q O HOH . C HOH 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.001 ? 
metalc ? metalc4 I MG MG . C MG 601 1_555 Q O HOH . C HOH 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.982 ? 
metalc ? metalc5 I MG MG . C MG 601 1_555 Q O HOH . C HOH 712 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.614 ? 
#
_chem_comp.formula           'C11 H26 N2 O6' 
_chem_comp.formula_weight    282.334 
_chem_comp.id                B3P 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL 
_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
C1 C2 B3P sing 70 n n 
C1 C3 B3P sing 71 n n 
C1 H11 B3P sing 72 n n 
C1 H12 B3P sing 73 n n 
C2 N2 B3P sing 74 n n 
C2 H21 B3P sing 75 n n 
C2 H22 B3P sing 76 n n 
C3 N1 B3P sing 77 n n 
C3 H31 B3P sing 78 n n 
C3 H32 B3P sing 79 n n 
N1 C4 B3P sing 80 n n 
N1 HN1 B3P sing 81 n n 
C4 C5 B3P sing 82 n n 
C4 C6 B3P sing 83 n n 
C4 C7 B3P sing 84 n n 
C5 O4 B3P sing 85 n n 
C5 H51 B3P sing 86 n n 
C5 H52 B3P sing 87 n n 
C6 O5 B3P sing 88 n n 
C6 H61 B3P sing 89 n n 
C6 H62 B3P sing 90 n n 
C7 O6 B3P sing 91 n n 
C7 H71 B3P sing 92 n n 
C7 H72 B3P sing 93 n n 
N2 C8 B3P sing 94 n n 
N2 HN2 B3P sing 95 n n 
C8 C9 B3P sing 96 n n 
C8 C10 B3P sing 97 n n 
C8 C11 B3P sing 98 n n 
C9 O1 B3P sing 99 n n 
C9 H91 B3P sing 100 n n 
C9 H92 B3P sing 101 n n 
C10 O2 B3P sing 102 n n 
C10 H101 B3P sing 103 n n 
C10 H102 B3P sing 104 n n 
C11 O3 B3P sing 105 n n 
C11 H111 B3P sing 106 n n 
C11 H112 B3P sing 107 n n 
O1 HO1 B3P sing 108 n n 
O2 HO2 B3P sing 109 n n 
O3 HO3 B3P sing 110 n n 
O4 HO4 B3P sing 111 n n 
O5 HO5 B3P sing 112 n n 
O6 HO6 B3P sing 113 n n 
#
_atom_sites.entry_id                     5KND 
_atom_sites.fract_transf_matrix[1][1]    0.007799 
_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]    0.007791 
_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]    0.004385 
_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
I 5 MG C 1 601 601 MG MG . 
J 6 GOL C 1 602 602 GOL GOL . 
K 7 PO4 C 1 603 603 PO4 PO4 . 
L 6 GOL F 1 501 501 GOL GOL . 
M 8 B3P F 1 502 502 B3P B3P . 
N 6 GOL G 1 301 301 GOL GOL . 
O 9 HOH A 1 601 601 HOH HOH . 
O 9 HOH A 2 602 602 HOH HOH . 
O 9 HOH A 3 603 603 HOH HOH . 
O 9 HOH A 4 604 604 HOH HOH . 
O 9 HOH A 5 605 605 HOH HOH . 
O 9 HOH A 6 606 606 HOH HOH . 
O 9 HOH A 7 607 607 HOH HOH . 
O 9 HOH A 8 608 608 HOH HOH . 
O 9 HOH A 9 609 609 HOH HOH . 
O 9 HOH A 10 610 610 HOH HOH . 
O 9 HOH A 11 611 611 HOH HOH . 
O 9 HOH A 12 612 612 HOH HOH . 
O 9 HOH A 13 613 613 HOH HOH . 
O 9 HOH A 14 614 614 HOH HOH . 
P 9 HOH B 1 601 601 HOH HOH . 
P 9 HOH B 2 602 602 HOH HOH . 
P 9 HOH B 3 603 603 HOH HOH . 
P 9 HOH B 4 604 604 HOH HOH . 
P 9 HOH B 5 605 605 HOH HOH . 
P 9 HOH B 6 606 606 HOH HOH . 
P 9 HOH B 7 607 607 HOH HOH . 
P 9 HOH B 8 608 608 HOH HOH . 
P 9 HOH B 9 609 609 HOH HOH . 
P 9 HOH B 10 610 610 HOH HOH . 
P 9 HOH B 11 611 611 HOH HOH . 
P 9 HOH B 12 612 612 HOH HOH . 
P 9 HOH B 13 613 613 HOH HOH . 
P 9 HOH B 14 614 614 HOH HOH . 
Q 9 HOH C 1 701 701 HOH HOH . 
Q 9 HOH C 2 702 702 HOH HOH . 
Q 9 HOH C 3 703 703 HOH HOH . 
Q 9 HOH C 4 704 704 HOH HOH . 
Q 9 HOH C 5 705 705 HOH HOH . 
Q 9 HOH C 6 706 706 HOH HOH . 
Q 9 HOH C 7 707 707 HOH HOH . 
Q 9 HOH C 8 708 708 HOH HOH . 
Q 9 HOH C 9 709 709 HOH HOH . 
Q 9 HOH C 10 710 710 HOH HOH . 
Q 9 HOH C 11 711 711 HOH HOH . 
Q 9 HOH C 12 712 712 HOH HOH . 
Q 9 HOH C 13 713 713 HOH HOH . 
Q 9 HOH C 14 714 714 HOH HOH . 
Q 9 HOH C 15 715 715 HOH HOH . 
Q 9 HOH C 16 716 716 HOH HOH . 
Q 9 HOH C 17 717 717 HOH HOH . 
Q 9 HOH C 18 718 718 HOH HOH . 
R 9 HOH D 1 501 501 HOH HOH . 
R 9 HOH D 2 502 502 HOH HOH . 
S 9 HOH E 1 501 501 HOH HOH . 
S 9 HOH E 2 502 502 HOH HOH . 
S 9 HOH E 3 503 503 HOH HOH . 
S 9 HOH E 4 504 504 HOH HOH . 
S 9 HOH E 5 505 505 HOH HOH . 
S 9 HOH E 6 506 506 HOH HOH . 
S 9 HOH E 7 507 507 HOH HOH . 
S 9 HOH E 8 508 508 HOH HOH . 
T 9 HOH F 1 601 601 HOH HOH . 
T 9 HOH F 2 602 602 HOH HOH . 
T 9 HOH F 3 603 603 HOH HOH . 
T 9 HOH F 4 604 604 HOH HOH . 
T 9 HOH F 5 605 605 HOH HOH . 
U 9 HOH G 1 401 401 HOH HOH . 
U 9 HOH G 2 402 402 HOH HOH . 
V 9 HOH H 1 201 201 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 C C1 B3P . . . M 8 58.29 48.185 51.258 1 69.96 ? C1 B3P 502 F 1 
HETATM 2 C C2 B3P . . . M 8 57.174 47.508 50.466 1 70.4 ? C2 B3P 502 F 1 
HETATM 3 C C3 B3P . . . M 8 59.637 47.63 50.8 1 69.54 ? C3 B3P 502 F 1 
HETATM 4 N N1 B3P . . . M 8 60.796 48.222 51.447 1 69.53 ? N1 B3P 502 F 1 
HETATM 5 C C4 B3P . . . M 8 62.107 47.66 51.167 1 69.7 ? C4 B3P 502 F 1 
HETATM 6 C C5 B3P . . . M 8 63.181 48.584 51.726 1 70.25 ? C5 B3P 502 F 1 
HETATM 7 C C6 B3P . . . M 8 62.224 46.273 51.787 1 69.3 ? C6 B3P 502 F 1 
HETATM 8 C C7 B3P . . . M 8 62.273 47.561 49.654 1 69.7 ? C7 B3P 502 F 1 
HETATM 9 N N2 B3P . . . M 8 55.843 47.695 51.015 1 71.09 ? N2 B3P 502 F 1 
HETATM 10 C C8 B3P . . . M 8 54.755 46.89 50.486 1 71.79 ? C8 B3P 502 F 1 
HETATM 11 C C9 B3P . . . M 8 53.444 47.213 51.197 1 71.6 ? C9 B3P 502 F 1 
HETATM 12 C C10 B3P . . . M 8 55.095 45.413 50.666 1 72.12 ? C10 B3P 502 F 1 
HETATM 13 C C11 B3P . . . M 8 54.622 47.191 48.996 1 72.17 ? C11 B3P 502 F 1 
HETATM 14 O O1 B3P . . . M 8 52.793 48.328 50.575 1 71.51 ? O1 B3P 502 F 1 
HETATM 15 O O2 B3P . . . M 8 55.205 45.093 52.059 1 72.27 ? O2 B3P 502 F 1 
HETATM 16 O O3 B3P . . . M 8 54.572 48.608 48.781 1 72.3 ? O3 B3P 502 F 1 
HETATM 17 O O4 B3P . . . M 8 64.057 47.836 52.575 1 70.78 ? O4 B3P 502 F 1 
HETATM 18 O O5 B3P . . . M 8 62.201 46.36 53.216 1 69.05 ? O5 B3P 502 F 1 
HETATM 19 O O6 B3P . . . M 8 63.473 48.226 49.24 1 69.5 ? O6 B3P 502 F 1 
#
_model_server_stats.io_time_ms              129 
_model_server_stats.parse_time_ms           17 
_model_server_stats.create_model_time_ms    45 
_model_server_stats.query_time_ms           305 
_model_server_stats.encode_time_ms          8 
_model_server_stats.element_count           19 
#