data_1KYX
#
_model_server_result.job_id            1nZDhZzYJxO9j4PRQJuBXA 
_model_server_result.datetime_utc      '2024-12-26 15:19:41' 
_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          1kyx 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"M","auth_seq_id":504}' 
#
_entry.id    1KYX 
#
_exptl.entry_id    1KYX 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              386.314 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '3-[8-((2S,3S,4R)-2,3,4,5-TETRAHYDROXYPENTYL)-2,4,7-TRIOXO-1,3,8-TRIHYDROPTERIDIN-6-YL]PROPANOIC ACID' 
_entity.pdbx_number_of_molecules    5 
_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            1KYX 
_cell.length_a            111.087 
_cell.length_b            145.178 
_cell.length_c            128.554 
_cell.Z_PDB               40 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1KYX 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        20 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 2 2 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 pentameric 5 author_and_software_defined_assembly 1 
PISA decameric 10 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' 3_655 -x+1,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 111.087 0 64.277 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 H N N 
? 3 I N N 
? 3 K N N 
? 3 M N N 
? 3 O N N 
#
_chem_comp.formula           'C14 H18 N4 O9' 
_chem_comp.formula_weight    386.314 
_chem_comp.id                CRM 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '3-[8-((2S,3S,4R)-2,3,4,5-TETRAHYDROXYPENTYL)-2,4,7-TRIOXO-1,3,8-TRIHYDROPTERIDIN-6-YL]PROPANOIC ACID' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     CARBOXYETHYLLUMAZINE 
#
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
C2 O15 CRM doub 70 n n 
C2 N3 CRM sing 71 n y 
C2 N1 CRM sing 72 n y 
N3 C4 CRM sing 73 n y 
N3 H3 CRM sing 74 n n 
C4 N10 CRM sing 75 n y 
C4 C5 CRM doub 76 n y 
N10 C17 CRM sing 77 n n 
N10 C9 CRM sing 78 n y 
C17 C18 CRM sing 79 n n 
C17 H171 CRM sing 80 n n 
C17 H172 CRM sing 81 n n 
C18 C20 CRM sing 82 n n 
C18 O19 CRM sing 83 n n 
C18 H18 CRM sing 84 n n 
C20 C22 CRM sing 85 n n 
C20 O21 CRM sing 86 n n 
C20 H20 CRM sing 87 n n 
C22 C25 CRM sing 88 n n 
C22 O23 CRM sing 89 n n 
C22 H22 CRM sing 90 n n 
C25 O26 CRM sing 91 n n 
C25 H251 CRM sing 92 n n 
C25 H252 CRM sing 93 n n 
O26 H26 CRM sing 94 n n 
O23 H23 CRM sing 95 n n 
O21 H21 CRM sing 96 n n 
O19 H19 CRM sing 97 n n 
C9 O16 CRM doub 98 n n 
C9 C8 CRM sing 99 n y 
C8 C11 CRM sing 100 n n 
C8 N7 CRM doub 101 n y 
C11 C12 CRM sing 102 n n 
C11 H111 CRM sing 103 n n 
C11 H112 CRM sing 104 n n 
C12 C13 CRM sing 105 n n 
C12 H121 CRM sing 106 n n 
C12 H122 CRM sing 107 n n 
C13 O28 CRM sing 108 n n 
C13 O27 CRM doub 109 n n 
O28 H28 CRM sing 110 n n 
N7 C5 CRM sing 111 n y 
C5 C6 CRM sing 112 n y 
C6 O14 CRM doub 113 n n 
C6 N1 CRM sing 114 n y 
N1 H1 CRM sing 115 n n 
#
_atom_sites.entry_id                     1KYX 
_atom_sites.fract_transf_matrix[1][1]    0.009002 
_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]    0.006888 
_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]    0.007779 
_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
F 2 PO4 A 1 1001 1 PO4 PO4 . 
G 2 PO4 A 1 1002 2 PO4 PO4 . 
H 3 CRM A 1 501 1 CRM CRB . 
I 3 CRM B 1 502 2 CRM CRB . 
J 2 PO4 C 1 1003 3 PO4 PO4 . 
K 3 CRM C 1 503 3 CRM CRB . 
L 2 PO4 D 1 1004 4 PO4 PO4 . 
M 3 CRM D 1 504 4 CRM CRB . 
N 2 PO4 E 1 1005 5 PO4 PO4 . 
O 3 CRM E 1 505 5 CRM CRB . 
P 4 HOH A 1 1003 1 HOH HOH . 
P 4 HOH A 2 1004 13 HOH HOH . 
P 4 HOH A 3 1005 17 HOH HOH . 
P 4 HOH A 4 1006 19 HOH HOH . 
P 4 HOH A 5 1007 20 HOH HOH . 
P 4 HOH A 6 1008 22 HOH HOH . 
P 4 HOH A 7 1009 24 HOH HOH . 
P 4 HOH A 8 1010 25 HOH HOH . 
P 4 HOH A 9 1011 27 HOH HOH . 
P 4 HOH A 10 1012 31 HOH HOH . 
P 4 HOH A 11 1013 33 HOH HOH . 
P 4 HOH A 12 1014 35 HOH HOH . 
P 4 HOH A 13 1015 36 HOH HOH . 
Q 4 HOH B 1 503 7 HOH HOH . 
Q 4 HOH B 2 504 12 HOH HOH . 
Q 4 HOH B 3 505 15 HOH HOH . 
Q 4 HOH B 4 506 21 HOH HOH . 
Q 4 HOH B 5 507 29 HOH HOH . 
Q 4 HOH B 6 508 30 HOH HOH . 
Q 4 HOH B 7 509 32 HOH HOH . 
Q 4 HOH B 8 510 39 HOH HOH . 
Q 4 HOH B 9 511 41 HOH HOH . 
R 4 HOH C 1 1004 3 HOH HOH . 
R 4 HOH C 2 1005 4 HOH HOH . 
R 4 HOH C 3 1006 5 HOH HOH . 
R 4 HOH C 4 1007 8 HOH HOH . 
R 4 HOH C 5 1008 11 HOH HOH . 
R 4 HOH C 6 1009 18 HOH HOH . 
R 4 HOH C 7 1010 38 HOH HOH . 
R 4 HOH C 8 1011 40 HOH HOH . 
R 4 HOH C 9 1012 42 HOH HOH . 
R 4 HOH C 10 1013 43 HOH HOH . 
S 4 HOH D 1 1005 2 HOH HOH . 
S 4 HOH D 2 1006 9 HOH HOH . 
S 4 HOH D 3 1007 10 HOH HOH . 
S 4 HOH D 4 1008 14 HOH HOH . 
S 4 HOH D 5 1009 28 HOH HOH . 
S 4 HOH D 6 1010 34 HOH HOH . 
S 4 HOH D 7 1011 44 HOH HOH . 
S 4 HOH D 8 1012 45 HOH HOH . 
T 4 HOH E 1 1006 6 HOH HOH . 
T 4 HOH E 2 1007 16 HOH HOH . 
T 4 HOH E 3 1008 23 HOH HOH . 
T 4 HOH E 4 1009 26 HOH HOH . 
T 4 HOH E 5 1010 37 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 C2 CRM . . . M 3 60.65 40.862 8.991 1 46.55 ? C2 CRM 504 D 1 
HETATM 2 O O15 CRM . . . M 3 61.459 41.734 8.725 1 48.48 ? O15 CRM 504 D 1 
HETATM 3 N N3 CRM . . . M 3 60.841 39.571 8.584 1 45.97 ? N3 CRM 504 D 1 
HETATM 4 C C4 CRM . . . M 3 60 38.504 8.823 1 44.33 ? C4 CRM 504 D 1 
HETATM 5 N N10 CRM . . . M 3 60.223 37.25 8.406 1 42.62 ? N10 CRM 504 D 1 
HETATM 6 C C17 CRM . . . M 3 61.416 36.881 7.636 1 38.85 ? C17 CRM 504 D 1 
HETATM 7 C C18 CRM . . . M 3 62.783 36.522 8.259 1 40.09 ? C18 CRM 504 D 1 
HETATM 8 C C20 CRM . . . M 3 63.71 35.754 7.243 1 39.38 ? C20 CRM 504 D 1 
HETATM 9 C C22 CRM . . . M 3 63.244 34.299 7.009 1 36.23 ? C22 CRM 504 D 1 
HETATM 10 C C25 CRM . . . M 3 64.201 33.482 6.09 1 32.33 ? C25 CRM 504 D 1 
HETATM 11 O O26 CRM . . . M 3 65.576 33.733 6.438 1 32.69 ? O26 CRM 504 D 1 
HETATM 12 O O23 CRM . . . M 3 63.155 33.634 8.287 1 35.5 ? O23 CRM 504 D 1 
HETATM 13 O O21 CRM . . . M 3 63.738 36.455 5.961 1 42.27 ? O21 CRM 504 D 1 
HETATM 14 O O19 CRM . . . M 3 63.414 37.76 8.683 1 40.05 ? O19 CRM 504 D 1 
HETATM 15 C C9 CRM . . . M 3 59.349 36.257 8.691 1 45.14 ? C9 CRM 504 D 1 
HETATM 16 O O16 CRM . . . M 3 59.514 35.093 8.342 1 41.46 ? O16 CRM 504 D 1 
HETATM 17 C C8 CRM . . . M 3 58.097 36.515 9.471 1 49.72 ? C8 CRM 504 D 1 
HETATM 18 C C11 CRM . . . M 3 57.013 35.514 9.879 1 52.96 ? C11 CRM 504 D 1 
HETATM 19 C C12 CRM . . . M 3 57.28 34.714 11.181 1 59.53 ? C12 CRM 504 D 1 
HETATM 20 C C13 CRM . . . M 3 57.7 35.563 12.379 1 69.71 ? C13 CRM 504 D 1 
HETATM 21 O O28 CRM . . . M 3 56.786 36.046 13.112 1 70.57 ? O28 CRM 504 D 1 
HETATM 22 O O27 CRM . . . M 3 58.933 35.769 12.598 1 74.81 ? O27 CRM 504 D 1 
HETATM 23 N N7 CRM . . . M 3 57.927 37.747 9.849 1 46.87 ? N7 CRM 504 D 1 
HETATM 24 C C5 CRM . . . M 3 58.879 38.808 9.542 1 44.46 ? C5 CRM 504 D 1 
HETATM 25 C C6 CRM . . . M 3 58.608 40.185 10.016 1 45.99 ? C6 CRM 504 D 1 
HETATM 26 O O14 CRM . . . M 3 57.592 40.406 10.659 1 50.25 ? O14 CRM 504 D 1 
HETATM 27 N N1 CRM . . . M 3 59.525 41.155 9.709 1 46.76 ? N1 CRM 504 D 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    15 
_model_server_stats.query_time_ms           334 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           27 
#