8C8I: Human dUTPase

Human dUTPase in complex with a potent proteinaceous inhibitor (Stl). Determined by X-ray diffraction at 3.2 Å resolution. Released 1 May 2024.

Method: X-ray diffraction
Resolution: 3.2 Å
Organisms: Homo sapiens, Staphylococcus aureus
Chains: 6
Atoms: 6,111
Mol. weight: 94.19 kDa
Ligands: MG
Released: 1 May 2024

Explore 8C8I in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8C8I contains 54 α-helices and 42 β-strands across 6 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 4 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	26-30	5	1
α-helix	35-38	4
β-strand	39	1	2
β-strand	48-51	4	2
β-strand	56-58	3	3
β-strand	62-67	6	4
β-strand	70-73	4	1
α-helix	74-75	2
β-strand	78-83	6	2
α-helix	86-92	7
β-strand	94-97	4	4
β-strand	100-101	2	2
β-strand	110-115	6	4
β-strand	121-123	3	3
β-strand	128-136	9	2
β-strand	137	1	5
α-helix	140	1
β-strand	141-145	5	6

Chain B: 6 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	25-30	6	7
α-helix	35-38	4
β-strand	39	1	8
β-strand	47-51	5	8
β-strand	56-58	3	9
α-helix	59	1
β-strand	62-67	6	10
β-strand	70-73	4	7
α-helix	74-75	2
β-strand	78-83	6	8
α-helix	84-85	2
α-helix	86-92	7
β-strand	94-97	4	10
β-strand	100-101	2	8
β-strand	110-115	6	10
β-strand	121-123	3	9
β-strand	128-136	9	8
β-strand	137	1	2
α-helix	140-141	2
β-strand	142-144	3	1

Chain C: 5 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	25-30	6	6
α-helix	35-38	4
β-strand	39	1	5
β-strand	48-51	4	5
β-strand	56-58	3	11
β-strand	62-67	6	12
β-strand	70-73	4	6
α-helix	74-75	2
β-strand	78-83	6	5
α-helix	84-85	2
α-helix	86-92	7
β-strand	94-97	4	12
β-strand	100-101	2	5
β-strand	110-115	6	12
β-strand	121-123	3	11
β-strand	128-136	9	5
β-strand	137-138	2	8
α-helix	140	1
β-strand	141-145	5	7

Chains D, E and F: 13 helices, 0 β-strands

Element	Residues	Length
α-helix	9-11	3
α-helix	13-24	12
α-helix	29-36	8
α-helix	40-47	8
α-helix	52-54	3
α-helix	57-65	9
α-helix	69-82	14
α-helix	86-89	4
α-helix	91-107	17
α-helix	109-112	4
α-helix	118-131	14
α-helix	136-138	3
α-helix	141-151	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial	A, B, C	protein	128	Homo sapiens	P33316 (AlphaFold model)
Orf20	D, E, F	protein	147	Staphylococcus aureus	Q9F0J8 (AlphaFold model)

Sequence of entity 1 (A, B, C), FASTA

>8C8I_1 Deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial (chains A, B, C)
MQLRFARLSEHATAPTRGSARAAGYDLYSAYDYTIPPMEKAVVKTDIQIALPSGCYGRVA
PRSGLAAKHFIDVGAGVIDEDYRGNVGVVLFNFGKEKFEVKKGDRIAQLICERIFYPEIE
EVQALDDT

Sequence of entity 2 (D, E, F), FASTA

>8C8I_2 Orf20 (chains D, E, F)
MAELPTHYGTIIKTLRKYMKLTQSKLSERTGFSQNTISNHENGNRNIGVNEIEIYGKGLG
IPSYILHRISDEFKEKGYSPTLNDFGKFDKMYSYVNKAYYNDGDIYYSSYDLYDETIKLL
ELLKESKINVNDIDYDYVLKLYKQILS

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1

Primary citation

Full-length inhibitor protein is the most effective to perturb human dUTPase activity. Kohegyi, B., Toth, Z.S., Gal, E. et al. Sci Rep (2025) 15:4836-4836. DOI 10.1038/s41598-025-86131-7 · PubMed

Other PDB entries of the same protein (UniProt P33316 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3ARA 1.7 Å, Discovery of Novel Uracil Derivatives as Potent Human dUTPase Inhibitors
3ARN 1.8 Å, Human dUTPase in complex with novel uracil derivative
3EHW 1.8 Å, Human dUTPase in complex with alpha,beta-imido-dUTP and Mg2+: visualization of the…
5H4J 1.8 Å, Crystal structure of Human dUTPase in complex with N-[(1R)-1-[3-(Cyclopentyloxy)-phenyl]-…
4MZ6 1.88 Å, Structure of importin-alpha: dUTPase S11E NLS mutant complex
7PWJ 1.94 Å, dUTPase from human in complex with Stl
1Q5H 2.0 Å, Human dUTP Pyrophosphatase complex with dUDP
1Q5U 2.0 Å, Human dutp pyrophosphatase
24OK 2.01 Å, Crystal structure of human dUTPase complexed with Zinc.
4MZ5 2.1 Å, Structure of importin-alpha: dUTPase NLS complex
2HQU 2.2 Å, Human dUTPase in complex with alpha,beta-iminodUTP and magnesium ion

Browse structure collections

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