data_4YTZ
#
_model_server_result.job_id            4UJ2qQGaakIKqyWZUSRtWQ 
_model_server_result.datetime_utc      '2024-11-07 21:30:01' 
_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          4ytz 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"M","auth_seq_id":1404}' 
#
_entry.id    4YTZ 
#
_exptl.entry_id    4YTZ 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              168.11 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'URIC ACID' 
_entity.pdbx_number_of_molecules    2 
_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            4YTZ 
_cell.length_a            100.172 
_cell.length_b            139.123 
_cell.length_c            223.273 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4YTZ 
_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    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_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 
_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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 4 F N N 
? 4 M 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
disulf ? disulf1 B SG CYS 535 B CYS 535 1_555 B SG CYS 992 B CYS 992 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.116 ? 
metalc ? metalc1 A SG CYS 43 A CYS 43 1_555 D FE2 FES . A FES 1402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.326 ? 
metalc ? metalc2 A SG CYS 48 A CYS 48 1_555 D FE2 FES . A FES 1402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.189 ? 
metalc ? metalc3 A SG CYS 51 A CYS 51 1_555 D FE1 FES . A FES 1402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.225 ? 
metalc ? metalc4 A SG CYS 73 A CYS 73 1_555 D FE1 FES . A FES 1402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.261 ? 
metalc ? metalc5 A SG CYS 112 A CYS 112 1_555 C FE1 FES . A FES 1401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.249 ? 
metalc ? metalc6 A SG CYS 115 A CYS 115 1_555 C FE2 FES . A FES 1401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.124 ? 
metalc ? metalc7 A SG CYS 147 A CYS 147 1_555 C FE2 FES . A FES 1401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.44 ? 
metalc ? metalc8 A OE2 GLU 740 A GLU 740 1_555 I CA CA . A CA 1407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.897 ? 
metalc ? metalc9 A OH TYR 743 A TYR 743 1_555 I CA CA . A CA 1407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.944 ? 
metalc ? metalc10 A OG1 THR 836 A THR 836 1_555 I CA CA . A CA 1407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.74 ? 
metalc ? metalc11 A O GLY 837 A GLY 837 1_555 I CA CA . A CA 1407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.775 ? 
metalc ? metalc12 A O GLY 867 A GLY 867 1_555 H CA CA . A CA 1406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.595 ? 
metalc ? metalc13 A O THR 870 A THR 870 1_555 H CA CA . A CA 1406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.798 ? 
metalc ? metalc14 A O GLU 871 A GLU 871 1_555 H CA CA . A CA 1406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.649 ? 
metalc ? metalc15 A OG SER 874 A SER 874 1_555 H CA CA . A CA 1406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.713 ? 
metalc ? metalc16 A OG SER 907 A SER 907 1_555 H CA CA . A CA 1406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.743 ? 
metalc ? metalc17 A O ASN 908 A ASN 908 1_555 H CA CA . A CA 1406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.798 ? 
metalc ? metalc18 B SG CYS 43 B CYS 43 1_555 K FE2 FES . B FES 1402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.318 ? 
metalc ? metalc19 B SG CYS 48 B CYS 48 1_555 K FE2 FES . B FES 1402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? 
metalc ? metalc20 B SG CYS 51 B CYS 51 1_555 K FE1 FES . B FES 1402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.258 ? 
metalc ? metalc21 B SG CYS 73 B CYS 73 1_555 K FE1 FES . B FES 1402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.358 ? 
metalc ? metalc22 B SG CYS 112 B CYS 112 1_555 J FE1 FES . B FES 1401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.286 ? 
metalc ? metalc23 B SG CYS 115 B CYS 115 1_555 J FE2 FES . B FES 1401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.239 ? 
metalc ? metalc24 B SG CYS 147 B CYS 147 1_555 J FE2 FES . B FES 1401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.377 ? 
metalc ? metalc25 B OE1 GLU 740 B GLU 740 1_555 P CA CA . B CA 1407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.125 ? 
metalc ? metalc26 B OE2 GLU 740 B GLU 740 1_555 P CA CA . B CA 1407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.844 ? 
metalc ? metalc27 B OH TYR 743 B TYR 743 1_555 P CA CA . B CA 1407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.875 ? 
metalc ? metalc28 B OG1 THR 836 B THR 836 1_555 P CA CA . B CA 1407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.76 ? 
metalc ? metalc29 B O GLY 837 B GLY 837 1_555 P CA CA . B CA 1407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.657 ? 
metalc ? metalc30 B O GLY 867 B GLY 867 1_555 O CA CA . B CA 1406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.767 ? 
metalc ? metalc31 B O THR 870 B THR 870 1_555 O CA CA . B CA 1406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.687 ? 
metalc ? metalc32 B O GLU 871 B GLU 871 1_555 O CA CA . B CA 1406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.003 ? 
metalc ? metalc33 B OG SER 874 B SER 874 1_555 O CA CA . B CA 1406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.511 ? 
metalc ? metalc34 B OG SER 907 B SER 907 1_555 O CA CA . B CA 1406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.786 ? 
metalc ? metalc35 B O ASN 908 B ASN 908 1_555 O CA CA . B CA 1406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.752 ? 
#
_chem_comp.formula           'C5 H4 N4 O3' 
_chem_comp.formula_weight    168.11 
_chem_comp.id                URC 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'URIC ACID' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     7,9-DIHYDRO-1H-PURINE-2,6,8(3H)-TRIONE 
#
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 URC sing 457 n y 
N1 C6 URC sing 458 n y 
N1 HN1 URC sing 459 n n 
C2 N3 URC sing 460 n y 
C2 O11 URC doub 461 n n 
C6 C5 URC sing 462 n y 
C6 O13 URC doub 463 n n 
N3 C4 URC sing 464 n y 
N3 HN3 URC sing 465 n n 
C4 C5 URC doub 466 n y 
C4 N9 URC sing 467 n y 
C5 N7 URC sing 468 n y 
N9 C8 URC sing 469 n y 
N9 HN9 URC sing 470 n n 
N7 C8 URC sing 471 n y 
N7 HN7 URC sing 472 n n 
C8 O24 URC doub 473 n n 
#
_atom_sites.entry_id                     4YTZ 
_atom_sites.fract_transf_matrix[1][1]    0.009983 
_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]    0.007188 
_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]    0.004479 
_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
C 2 FES A 1 1401 1 FES FES . 
D 2 FES A 1 1402 2 FES FES . 
E 3 FAD A 1 1403 4006 FAD FAD . 
F 4 URC A 1 1404 1 URC URC . 
G 5 BCT A 1 1405 1 BCT BCT . 
H 6 CA A 1 1406 1 CA CA . 
I 6 CA A 1 1407 3 CA CA . 
J 2 FES B 1 1401 1 FES FES . 
K 2 FES B 1 1402 2 FES FES . 
L 3 FAD B 1 1403 3006 FAD FAD . 
M 4 URC B 1 1404 2 URC URC . 
N 5 BCT B 1 1405 2 BCT BCT . 
O 6 CA B 1 1406 2 CA CA . 
P 6 CA B 1 1407 4 CA CA . 
Q 7 HOH A 1 1501 16 HOH HOH . 
Q 7 HOH A 2 1502 32 HOH HOH . 
Q 7 HOH A 3 1503 9 HOH HOH . 
Q 7 HOH A 4 1504 65 HOH HOH . 
Q 7 HOH A 5 1505 28 HOH HOH . 
Q 7 HOH A 6 1506 18 HOH HOH . 
Q 7 HOH A 7 1507 21 HOH HOH . 
Q 7 HOH A 8 1508 74 HOH HOH . 
Q 7 HOH A 9 1509 50 HOH HOH . 
Q 7 HOH A 10 1510 59 HOH HOH . 
Q 7 HOH A 11 1511 57 HOH HOH . 
Q 7 HOH A 12 1512 1 HOH HOH . 
Q 7 HOH A 13 1513 83 HOH HOH . 
Q 7 HOH A 14 1514 20 HOH HOH . 
Q 7 HOH A 15 1515 84 HOH HOH . 
Q 7 HOH A 16 1516 47 HOH HOH . 
Q 7 HOH A 17 1517 4 HOH HOH . 
Q 7 HOH A 18 1518 3 HOH HOH . 
Q 7 HOH A 19 1519 54 HOH HOH . 
Q 7 HOH A 20 1520 81 HOH HOH . 
Q 7 HOH A 21 1521 56 HOH HOH . 
Q 7 HOH A 22 1522 13 HOH HOH . 
Q 7 HOH A 23 1523 24 HOH HOH . 
Q 7 HOH A 24 1524 58 HOH HOH . 
Q 7 HOH A 25 1525 82 HOH HOH . 
Q 7 HOH A 26 1526 22 HOH HOH . 
Q 7 HOH A 27 1527 33 HOH HOH . 
Q 7 HOH A 28 1528 39 HOH HOH . 
Q 7 HOH A 29 1529 55 HOH HOH . 
Q 7 HOH A 30 1530 69 HOH HOH . 
Q 7 HOH A 31 1531 7 HOH HOH . 
Q 7 HOH A 32 1532 49 HOH HOH . 
Q 7 HOH A 33 1533 13 HOH HOH . 
Q 7 HOH A 34 1534 7 HOH HOH . 
Q 7 HOH A 35 1535 8 HOH HOH . 
Q 7 HOH A 36 1536 10 HOH HOH . 
Q 7 HOH A 37 1537 3 HOH HOH . 
Q 7 HOH A 38 1538 2 HOH HOH . 
Q 7 HOH A 39 1539 6 HOH HOH . 
Q 7 HOH A 40 1540 5 HOH HOH . 
R 7 HOH B 1 1501 23 HOH HOH . 
R 7 HOH B 2 1502 30 HOH HOH . 
R 7 HOH B 3 1503 21 HOH HOH . 
R 7 HOH B 4 1504 53 HOH HOH . 
R 7 HOH B 5 1505 78 HOH HOH . 
R 7 HOH B 6 1506 73 HOH HOH . 
R 7 HOH B 7 1507 14 HOH HOH . 
R 7 HOH B 8 1508 35 HOH HOH . 
R 7 HOH B 9 1509 68 HOH HOH . 
R 7 HOH B 10 1510 66 HOH HOH . 
R 7 HOH B 11 1511 51 HOH HOH . 
R 7 HOH B 12 1512 25 HOH HOH . 
R 7 HOH B 13 1513 12 HOH HOH . 
R 7 HOH B 14 1514 27 HOH HOH . 
R 7 HOH B 15 1515 79 HOH HOH . 
R 7 HOH B 16 1516 34 HOH HOH . 
R 7 HOH B 17 1517 36 HOH HOH . 
R 7 HOH B 18 1518 44 HOH HOH . 
R 7 HOH B 19 1519 60 HOH HOH . 
R 7 HOH B 20 1520 9 HOH HOH . 
R 7 HOH B 21 1521 15 HOH HOH . 
R 7 HOH B 22 1522 62 HOH HOH . 
R 7 HOH B 23 1523 17 HOH HOH . 
R 7 HOH B 24 1524 40 HOH HOH . 
R 7 HOH B 25 1525 45 HOH HOH . 
R 7 HOH B 26 1526 19 HOH HOH . 
R 7 HOH B 27 1527 43 HOH HOH . 
R 7 HOH B 28 1528 26 HOH HOH . 
R 7 HOH B 29 1529 8 HOH HOH . 
R 7 HOH B 30 1530 48 HOH HOH . 
R 7 HOH B 31 1531 71 HOH HOH . 
R 7 HOH B 32 1532 15 HOH HOH . 
R 7 HOH B 33 1533 80 HOH HOH . 
R 7 HOH B 34 1534 37 HOH HOH . 
R 7 HOH B 35 1535 2 HOH HOH . 
R 7 HOH B 36 1536 70 HOH HOH . 
R 7 HOH B 37 1537 77 HOH HOH . 
R 7 HOH B 38 1538 72 HOH HOH . 
R 7 HOH B 39 1539 67 HOH HOH . 
R 7 HOH B 40 1540 31 HOH HOH . 
R 7 HOH B 41 1541 38 HOH HOH . 
R 7 HOH B 42 1542 29 HOH HOH . 
R 7 HOH B 43 1543 52 HOH HOH . 
R 7 HOH B 44 1544 46 HOH HOH . 
R 7 HOH B 45 1545 41 HOH HOH . 
R 7 HOH B 46 1546 14 HOH HOH . 
R 7 HOH B 47 1547 61 HOH HOH . 
R 7 HOH B 48 1548 42 HOH HOH . 
R 7 HOH B 49 1549 63 HOH HOH . 
R 7 HOH B 50 1550 4 HOH HOH . 
R 7 HOH B 51 1551 64 HOH HOH . 
R 7 HOH B 52 1552 17 HOH HOH . 
R 7 HOH B 53 1553 6 HOH HOH . 
R 7 HOH B 54 1554 1 HOH HOH . 
R 7 HOH B 55 1555 12 HOH HOH . 
R 7 HOH B 56 1556 75 HOH HOH . 
R 7 HOH B 57 1557 10 HOH HOH . 
R 7 HOH B 58 1558 5 HOH HOH . 
R 7 HOH B 59 1559 76 HOH HOH . 
R 7 HOH B 60 1560 18 HOH HOH . 
R 7 HOH B 61 1561 20 HOH HOH . 
R 7 HOH B 62 1562 11 HOH HOH . 
R 7 HOH B 63 1563 16 HOH HOH . 
R 7 HOH B 64 1564 19 HOH HOH . 
R 7 HOH B 65 1565 11 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 URC . . . M 4 9.614 -10.345 67.441 1 31.19 ? N1 URC 1404 B 1 
HETATM 2 C C2 URC . . . M 4 8.865 -11.21 68.18 1 34.27 ? C2 URC 1404 B 1 
HETATM 3 C C6 URC . . . M 4 10.953 -10.453 67.379 1 34.77 ? C6 URC 1404 B 1 
HETATM 4 N N3 URC . . . M 4 9.394 -12.247 68.892 1 34.11 ? N3 URC 1404 B 1 
HETATM 5 O O11 URC . . . M 4 7.517 -11.034 68.196 1 34.71 ? O11 URC 1404 B 1 
HETATM 6 C C4 URC . . . M 4 10.738 -12.414 68.87 1 37.23 ? C4 URC 1404 B 1 
HETATM 7 C C5 URC . . . M 4 11.573 -11.567 68.139 1 37.63 ? C5 URC 1404 B 1 
HETATM 8 N N9 URC . . . M 4 11.48 -13.363 69.505 1 37.33 ? N9 URC 1404 B 1 
HETATM 9 O O13 URC . . . M 4 11.742 -9.593 66.654 1 33.26 ? O13 URC 1404 B 1 
HETATM 10 N N7 URC . . . M 4 12.848 -11.978 68.333 1 38.04 ? N7 URC 1404 B 1 
HETATM 11 C C8 URC . . . M 4 12.733 -13.048 69.147 1 37.03 ? C8 URC 1404 B 1 
HETATM 12 O O24 URC . . . M 4 13.91 -13.799 69.625 1 36.51 ? O24 URC 1404 B 1 
#
_model_server_stats.io_time_ms              67 
_model_server_stats.parse_time_ms           14 
_model_server_stats.create_model_time_ms    35 
_model_server_stats.query_time_ms           312 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           12 
#