3EHW: Human dUTPase

Human dUTPase in complex with alpha,beta-imido-dUTP and Mg2+: visualization of the full-length C-termini in all monomers and suggestion for an additional metal ion binding site. Determined by X-ray diffraction at 1.8 Å resolution. Released 30 Sept 2008.

Method: X-ray diffraction
Resolution: 1.8 Å
Organism: Homo sapiens
Chains: 6
Atoms: 7,277
Mol. weight: 109.62 kDa
Ligands: MG, DUP
Released: 30 Sept 2008

Explore 3EHW in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3EHW contains 24 α-helices and 94 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, 16 β-strands

Element	Residues	Length	Sheet
β-strand	26-30	5	1
β-strand	39-40	2	2
β-strand	47-51	5	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	105	1	5
β-strand	110-115	6	4
β-strand	121-123	3	3
β-strand	128-136	9	2
β-strand	137	1	6
α-helix	140-141	2
β-strand	142-144	3	7
α-helix	148-150	3
β-strand	154	1	8

Chain B: 4 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	26-30	5	9
β-strand	39	1	10
β-strand	47-51	5	10
β-strand	56-58	3	11
β-strand	62-67	6	12
β-strand	70-73	4	9
α-helix	74-75	2
β-strand	78-83	6	10
α-helix	86-92	7
β-strand	94-97	4	12
β-strand	100-101	2	10
β-strand	105	1	13
β-strand	110-115	6	12
β-strand	121-123	3	11
β-strand	128-136	9	10
β-strand	137-138	2	2
α-helix	140-141	2
β-strand	142-144	3	1
α-helix	148-150	3
β-strand	154	1	5

Chain C: 3 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	26-30	5	7
β-strand	39-40	2	6
β-strand	47-51	5	6
β-strand	56-58	3	14
β-strand	62-67	6	15
β-strand	70-73	4	7
α-helix	74-75	2
β-strand	78-83	6	6
α-helix	86-92	7
β-strand	94-97	4	15
β-strand	100-101	2	6
β-strand	105	1	8
β-strand	110-115	6	15
β-strand	121-123	3	14
β-strand	128-136	9	6
β-strand	137	1	10
α-helix	140-141	2
β-strand	142-144	3	9
β-strand	154	1	13

Chain X: 4 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	26-30	5	16
β-strand	39-40	2	17
β-strand	47-51	5	17
β-strand	56-58	3	18
β-strand	62-67	6	19
β-strand	70-73	4	16
α-helix	74-75	2
β-strand	78-83	6	17
α-helix	86-92	7
β-strand	94-97	4	19
β-strand	100-101	2	17
β-strand	105	1	20
β-strand	110-115	6	19
β-strand	121-123	3	18
β-strand	128-136	9	17
β-strand	137-138	2	21
α-helix	140-141	2
β-strand	142-144	3	22
α-helix	148-150	3
β-strand	154	1	23

Chain Y: 4 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	26-30	5	24
β-strand	39-40	2	25
β-strand	47-51	5	25
β-strand	56-58	3	26
β-strand	62-67	6	27
β-strand	70-73	4	24
α-helix	74-75	2
β-strand	78-83	6	25
α-helix	86-92	7
β-strand	94-97	4	27
β-strand	100-101	2	25
β-strand	110-115	6	27
β-strand	121-123	3	26
β-strand	128-136	9	25
β-strand	137	1	17
α-helix	140-141	2
β-strand	142-144	3	16
α-helix	148-150	3
β-strand	154	1	20

Chain Z: 5 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	26-30	5	22
β-strand	39-40	2	21
β-strand	47-51	5	21
α-helix	52	1
β-strand	56-58	3	28
β-strand	62-67	6	29
β-strand	70-73	4	22
α-helix	74-75	2
β-strand	78-83	6	21
α-helix	86-92	7
β-strand	94-97	4	29
β-strand	100-101	2	21
β-strand	105	1	23
β-strand	110-115	6	29
β-strand	121-123	3	28
β-strand	128-136	9	21
β-strand	137-138	2	25
α-helix	140-141	2
β-strand	142-144	3	24
α-helix	148-150	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
dUTP pyrophosphatase	A, B, C, X, Y, Z	protein	164	Homo sapiens	P33316 (AlphaFold model)

Sequence of entity 1 (A, B, C, X, Y, Z), FASTA

>3EHW_1 dUTP pyrophosphatase (chains A, B, C, X, Y, Z)
MPCSEETPAISPSKRARPAEVGGMQLRFARLSEHATAPTRGSARAAGYDLYSAYDYTIPP
MEKAVVKTDIQIALPSGCYGRVAPRSGLAAKHFIDVGAGVIDEDYRGNVGVVLFNFGKEK
FEVKKGDRIAQLICERIFYPEIEEVQALDDTERGSGGFGSTGKN

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	8
DUP	2'-deoxyuridine 5'-alpha,beta-imido-triphosphate	C9 H16 N3 O13 P3	6

Primary citation

Human dUTPase in complex with alpha,beta-imido-dUTP and Mg2+: visualization of the full-length C-termini in all monomers and suggestion for an additional metal ion binding site. Takacs, E., Barabas, O., Vertessy, B.G. To be published.

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
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
8C8I 3.2 Å, Human dUTPase in complex with a potent proteinaceous inhibitor (Stl)

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