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Crystal structure of apo DUT1P from saccharomyces cerevisiae

Analyse Crystal structure of apo DUT1P from saccharomyces cerevisiae in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3HHQ
Type: protein
Length: 3,045 residues
Chains: 24
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Deoxyuridine 5'-triphosphate nucleotidohydrolase
EC: 3.6.1.23
UniProt: P33317
Ligands: NA, SO4, CL
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 11 distinct chains · 5% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23)	protein	126	6% helix, 47% strand	P33317
B	Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23)	protein	128	5% helix, 45% strand	P33317
C, E, T	Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23)	protein	128	5% helix, 46% strand	P33317
D, N, P, Q	Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23)	protein	125	6% helix, 46% strand	P33317
F, H, J, X	Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23)	protein	126	6% helix, 45% strand	P33317
G, O, R, U, V	Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23)	protein	127	6% helix, 46% strand	P33317
I	Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23)	protein	127	6% helix, 47% strand	P33317
K	Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23)	protein	127	6% helix, 45% strand	P33317
L, S	Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23)	protein	127	6% helix, 46% strand	P33317
M	Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23)	protein	130	5% helix, 44% strand	P33317
W	Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23)	protein	130	5% helix, 44% strand	P33317

Ligands and binding sites

NA · Sodium ion · metal · 14 copies · chains A, B, C, E, F, K, L, M, N, O, P, Q, S, U, T, V
SO4 · Sulfate ion · ion · 35 copies · chains A, B, C, D, E, F, G, K, H, I, X, J, L, M, N, O, Q, P, R, S, T, U, V, W
CL · Chloride ion · ion · 17 copies · chains B, C, D, E, F, I, J, L, N, Q, R, T, U, V
EDO · 1,2-ethanediol · additive · 34 copies · chains D, F, E, K, G, J, L, M, N, O, P, Q, R, S, T, U, V, X, W
PEG · Di(hydroxyethyl)ether · additive · 7 copies · chains H, K, J, L, D, M, N, O, W, X, F
GOL · Glycerol · additive · chains T, U

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	944	0.81	0.83	75	SO4
2	798	0.80	0.83	68	SO4
3	120	0.79	0.98	26	EDO
4	112	0.78	0.98	27	empty
5	114	0.78	0.98	30	EDO

Interfaces

64 interfaces between chains.

A–B · 1537 Å² buried · 22 hydrogen bonds · protein-protein
J–K · 1511 Å² buried · 21 hydrogen bonds · protein-protein
S–T · 1510 Å² buried · 16 hydrogen bonds · protein-protein
M–N · 1494 Å² buried · 18 hydrogen bonds · protein-protein
W–X · 1487 Å² buried · 19 hydrogen bonds · protein-protein

Compared structures

3HHQ · Crystal structure of apo dUT1p from Saccharomyces cerevisiae · the same entry in another collection · chain K against K, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P33317
Elsewhere: RCSB PDB 3HHQ · PDBe 3HHQ · UniProt P33317

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