data_5YLN
#
_model_server_result.job_id            HPZlk4hUSGw_WRMguoPROQ 
_model_server_result.datetime_utc      '2025-05-21 05:50:53' 
_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          5yln 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"M","auth_seq_id":403}' 
#
_entry.id    5YLN 
#
_exptl.entry_id    5YLN 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              122.143 
_entity.id                          3 
_entity.src_method                  man 
_entity.type                        non-polymer 
_entity.pdbx_description            2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL 
_entity.pdbx_number_of_molecules    4 
_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            5YLN 
_cell.length_a            88.177 
_cell.length_b            123.245 
_cell.length_c            130.356 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5YLN 
_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,Q,R 1 1 
C,D,K,L,M,N,O,P,S,T 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 G N N 
? 3 J N N 
? 3 M N N 
? 3 P 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 SG CYS 42 A CYS 38 1_555 E ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.527 ? 
metalc ? metalc2 A NE2 HIS 64 A HIS 60 1_555 E ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? 
metalc ? metalc3 A SG CYS 94 A CYS 90 1_555 F ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.341 ? 
metalc ? metalc4 A SG CYS 97 A CYS 93 1_555 F ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.363 ? 
metalc ? metalc5 A SG CYS 100 A CYS 96 1_555 F ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.228 ? 
metalc ? metalc6 A SG CYS 108 A CYS 104 1_555 F ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.381 ? 
metalc ? metalc7 E ZN ZN . A ZN 401 1_555 G N TRS . A TRS 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.981 ? 
metalc ? metalc8 B SG CYS 42 B CYS 38 1_555 H ZN ZN . B ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.383 ? 
metalc ? metalc9 B NE2 HIS 64 B HIS 60 1_555 H ZN ZN . B ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.098 ? 
metalc ? metalc10 B SG CYS 94 B CYS 90 1_555 I ZN ZN . B ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.479 ? 
metalc ? metalc11 B SG CYS 97 B CYS 93 1_555 I ZN ZN . B ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.396 ? 
metalc ? metalc12 B SG CYS 100 B CYS 96 1_555 I ZN ZN . B ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.23 ? 
metalc ? metalc13 B SG CYS 108 B CYS 104 1_555 I ZN ZN . B ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.268 ? 
metalc ? metalc14 H ZN ZN . B ZN 401 1_555 J N TRS . B TRS 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.998 ? 
metalc ? metalc15 C SG CYS 42 C CYS 38 1_555 K ZN ZN . C ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.56 ? 
metalc ? metalc16 C NE2 HIS 64 C HIS 60 1_555 K ZN ZN . C ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.131 ? 
metalc ? metalc17 C SG CYS 94 C CYS 90 1_555 L ZN ZN . C ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.552 ? 
metalc ? metalc18 C SG CYS 97 C CYS 93 1_555 L ZN ZN . C ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? 
metalc ? metalc19 C SG CYS 100 C CYS 96 1_555 L ZN ZN . C ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.418 ? 
metalc ? metalc20 C SG CYS 108 C CYS 104 1_555 L ZN ZN . C ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.295 ? 
metalc ? metalc21 K ZN ZN . C ZN 401 1_555 M N TRS . C TRS 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.98 ? 
metalc ? metalc22 D SG CYS 42 D CYS 38 1_555 N ZN ZN . D ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.508 ? 
metalc ? metalc23 D NE2 HIS 64 D HIS 60 1_555 N ZN ZN . D ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.197 ? 
metalc ? metalc24 D SG CYS 94 D CYS 90 1_555 O ZN ZN . D ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.391 ? 
metalc ? metalc25 D SG CYS 97 D CYS 93 1_555 O ZN ZN . D ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.318 ? 
metalc ? metalc26 D SG CYS 100 D CYS 96 1_555 O ZN ZN . D ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.412 ? 
metalc ? metalc27 D SG CYS 108 D CYS 104 1_555 O ZN ZN . D ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.264 ? 
metalc ? metalc28 N ZN ZN . D ZN 401 1_555 P N TRS . D TRS 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.825 ? 
#
_chem_comp.formula           'C4 H12 N O3 1' 
_chem_comp.formula_weight    122.143 
_chem_comp.id                TRS 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     'TRIS BUFFER' 
#
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
C C1 TRS sing 334 n n 
C C2 TRS sing 335 n n 
C C3 TRS sing 336 n n 
C N TRS sing 337 n n 
C1 O1 TRS sing 338 n n 
C1 H11 TRS sing 339 n n 
C1 H12 TRS sing 340 n n 
C2 O2 TRS sing 341 n n 
C2 H21 TRS sing 342 n n 
C2 H22 TRS sing 343 n n 
C3 O3 TRS sing 344 n n 
C3 H31 TRS sing 345 n n 
C3 H32 TRS sing 346 n n 
N HN1 TRS sing 347 n n 
N HN2 TRS sing 348 n n 
N HN3 TRS sing 349 n n 
O1 HO1 TRS sing 350 n n 
O2 HO2 TRS sing 351 n n 
O3 HO3 TRS sing 352 n n 
#
_atom_sites.entry_id                     5YLN 
_atom_sites.fract_transf_matrix[1][1]    0.011341 
_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]    0.008114 
_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]    0.007671 
_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 ZN A 1 401 355 ZN ZN . 
F 2 ZN A 1 402 356 ZN ZN . 
G 3 TRS A 1 403 357 TRS TRS . 
H 2 ZN B 1 401 355 ZN ZN . 
I 2 ZN B 1 402 356 ZN ZN . 
J 3 TRS B 1 403 357 TRS TRS . 
K 2 ZN C 1 401 355 ZN ZN . 
L 2 ZN C 1 402 356 ZN ZN . 
M 3 TRS C 1 403 357 TRS TRS . 
N 2 ZN D 1 401 355 ZN ZN . 
O 2 ZN D 1 402 356 ZN ZN . 
P 3 TRS D 1 403 357 TRS TRS . 
Q 4 HOH A 1 501 90 HOH HOH . 
Q 4 HOH A 2 502 63 HOH HOH . 
Q 4 HOH A 3 503 59 HOH HOH . 
Q 4 HOH A 4 504 19 HOH HOH . 
Q 4 HOH A 5 505 10 HOH HOH . 
Q 4 HOH A 6 506 100 HOH HOH . 
Q 4 HOH A 7 507 64 HOH HOH . 
Q 4 HOH A 8 508 9 HOH HOH . 
Q 4 HOH A 9 509 97 HOH HOH . 
Q 4 HOH A 10 510 25 HOH HOH . 
Q 4 HOH A 11 511 54 HOH HOH . 
Q 4 HOH A 12 512 75 HOH HOH . 
Q 4 HOH A 13 513 78 HOH HOH . 
Q 4 HOH A 14 514 42 HOH HOH . 
Q 4 HOH A 15 515 32 HOH HOH . 
Q 4 HOH A 16 516 96 HOH HOH . 
Q 4 HOH A 17 517 3 HOH HOH . 
Q 4 HOH A 18 518 47 HOH HOH . 
Q 4 HOH A 19 519 5 HOH HOH . 
Q 4 HOH A 20 520 15 HOH HOH . 
Q 4 HOH A 21 521 86 HOH HOH . 
Q 4 HOH A 22 522 105 HOH HOH . 
Q 4 HOH A 23 523 50 HOH HOH . 
Q 4 HOH A 24 524 17 HOH HOH . 
Q 4 HOH A 25 525 53 HOH HOH . 
Q 4 HOH A 26 526 52 HOH HOH . 
Q 4 HOH A 27 527 95 HOH HOH . 
Q 4 HOH A 28 528 62 HOH HOH . 
Q 4 HOH A 29 529 4 HOH HOH . 
Q 4 HOH A 30 530 34 HOH HOH . 
Q 4 HOH A 31 531 89 HOH HOH . 
Q 4 HOH A 32 532 103 HOH HOH . 
Q 4 HOH A 33 533 24 HOH HOH . 
R 4 HOH B 1 501 40 HOH HOH . 
R 4 HOH B 2 502 30 HOH HOH . 
R 4 HOH B 3 503 67 HOH HOH . 
R 4 HOH B 4 504 94 HOH HOH . 
R 4 HOH B 5 505 48 HOH HOH . 
R 4 HOH B 6 506 82 HOH HOH . 
R 4 HOH B 7 507 61 HOH HOH . 
R 4 HOH B 8 508 60 HOH HOH . 
R 4 HOH B 9 509 70 HOH HOH . 
R 4 HOH B 10 510 7 HOH HOH . 
R 4 HOH B 11 511 39 HOH HOH . 
R 4 HOH B 12 512 51 HOH HOH . 
R 4 HOH B 13 513 106 HOH HOH . 
R 4 HOH B 14 514 43 HOH HOH . 
R 4 HOH B 15 515 71 HOH HOH . 
R 4 HOH B 16 516 66 HOH HOH . 
R 4 HOH B 17 517 88 HOH HOH . 
R 4 HOH B 18 518 28 HOH HOH . 
R 4 HOH B 19 519 55 HOH HOH . 
R 4 HOH B 20 520 22 HOH HOH . 
R 4 HOH B 21 521 8 HOH HOH . 
R 4 HOH B 22 522 65 HOH HOH . 
R 4 HOH B 23 523 108 HOH HOH . 
S 4 HOH C 1 501 20 HOH HOH . 
S 4 HOH C 2 502 85 HOH HOH . 
S 4 HOH C 3 503 49 HOH HOH . 
S 4 HOH C 4 504 58 HOH HOH . 
S 4 HOH C 5 505 74 HOH HOH . 
S 4 HOH C 6 506 76 HOH HOH . 
S 4 HOH C 7 507 81 HOH HOH . 
S 4 HOH C 8 508 35 HOH HOH . 
S 4 HOH C 9 509 46 HOH HOH . 
S 4 HOH C 10 510 11 HOH HOH . 
S 4 HOH C 11 511 93 HOH HOH . 
S 4 HOH C 12 512 13 HOH HOH . 
S 4 HOH C 13 513 31 HOH HOH . 
S 4 HOH C 14 514 72 HOH HOH . 
S 4 HOH C 15 515 38 HOH HOH . 
S 4 HOH C 16 516 101 HOH HOH . 
S 4 HOH C 17 517 14 HOH HOH . 
S 4 HOH C 18 518 84 HOH HOH . 
S 4 HOH C 19 519 29 HOH HOH . 
S 4 HOH C 20 520 45 HOH HOH . 
S 4 HOH C 21 521 104 HOH HOH . 
S 4 HOH C 22 522 80 HOH HOH . 
S 4 HOH C 23 523 6 HOH HOH . 
S 4 HOH C 24 524 77 HOH HOH . 
S 4 HOH C 25 525 107 HOH HOH . 
S 4 HOH C 26 526 99 HOH HOH . 
S 4 HOH C 27 527 56 HOH HOH . 
S 4 HOH C 28 528 87 HOH HOH . 
S 4 HOH C 29 529 68 HOH HOH . 
T 4 HOH D 1 501 26 HOH HOH . 
T 4 HOH D 2 502 1 HOH HOH . 
T 4 HOH D 3 503 41 HOH HOH . 
T 4 HOH D 4 504 2 HOH HOH . 
T 4 HOH D 5 505 79 HOH HOH . 
T 4 HOH D 6 506 57 HOH HOH . 
T 4 HOH D 7 507 83 HOH HOH . 
T 4 HOH D 8 508 44 HOH HOH . 
T 4 HOH D 9 509 18 HOH HOH . 
T 4 HOH D 10 510 27 HOH HOH . 
T 4 HOH D 11 511 12 HOH HOH . 
T 4 HOH D 12 512 102 HOH HOH . 
T 4 HOH D 13 513 16 HOH HOH . 
T 4 HOH D 14 514 37 HOH HOH . 
T 4 HOH D 15 515 69 HOH HOH . 
T 4 HOH D 16 516 73 HOH HOH . 
T 4 HOH D 17 517 23 HOH HOH . 
T 4 HOH D 18 518 98 HOH HOH . 
T 4 HOH D 19 519 21 HOH HOH . 
T 4 HOH D 20 520 91 HOH HOH . 
T 4 HOH D 21 521 33 HOH HOH . 
T 4 HOH D 22 522 92 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 C TRS . . . M 3 -7.95 -18.715 -26.94 1 51.87 ? C TRS 403 C 1 
HETATM 2 C C1 TRS . . . M 3 -8.378 -19.31 -25.609 1 49.02 ? C1 TRS 403 C 1 
HETATM 3 C C2 TRS . . . M 3 -7.062 -17.487 -26.766 1 45.81 ? C2 TRS 403 C 1 
HETATM 4 C C3 TRS . . . M 3 -9.193 -18.362 -27.752 1 56.23 ? C3 TRS 403 C 1 
HETATM 5 N N TRS . . . M 3 -7.158 -19.742 -27.625 1 44.14 ? N TRS 403 C 1 
HETATM 6 O O1 TRS . . . M 3 -8.595 -20.684 -25.825 1 59.99 ? O1 TRS 403 C 1 
HETATM 7 O O2 TRS . . . M 3 -6.034 -17.837 -25.871 1 49.53 ? O2 TRS 403 C 1 
HETATM 8 O O3 TRS . . . M 3 -10.034 -19.492 -27.886 1 54.98 ? O3 TRS 403 C 1 
#
_model_server_stats.io_time_ms              23 
_model_server_stats.parse_time_ms           22 
_model_server_stats.create_model_time_ms    35 
_model_server_stats.query_time_ms           236 
_model_server_stats.encode_time_ms          10 
_model_server_stats.element_count           8 
#