1Q5H: Human dUTP Pyrophosphatase complex with dUDP

Human dUTP Pyrophosphatase complex with dUDP. Determined by X-ray diffraction at 2.0 Å resolution. Released 19 Aug 2003.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Homo sapiens
Chains: 3
Atoms: 3,463
Mol. weight: 49.92 kDa
Ligands: MG, DUD
Released: 19 Aug 2003

Explore 1Q5H in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1Q5H contains 12 α-helices and 44 β-strands across 3 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	2-7	6	1
β-strand	16-17	2	2
β-strand	24-28	5	2
β-strand	33-35	3	3
β-strand	39-44	6	4
β-strand	47-50	4	1
α-helix	51-52	2
β-strand	55-60	6	2
α-helix	63-69	7
β-strand	71-74	4	4
β-strand	77-78	2	2
β-strand	87-92	6	4
β-strand	98-100	3	3
α-helix	101	1
β-strand	105-113	9	2
β-strand	114	1	5
α-helix	117	1
β-strand	118-121	4	6

Chain B: 4 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	7
β-strand	16	1	8
β-strand	24-28	5	8
β-strand	33-35	3	9
β-strand	39-44	6	10
β-strand	47-50	4	7
α-helix	51-52	2
β-strand	55-60	6	8
α-helix	63-69	7
β-strand	71-74	4	10
β-strand	77-78	2	8
β-strand	82	1	11
β-strand	87-92	6	10
β-strand	98-100	3	9
β-strand	105-113	9	8
β-strand	114	1	2
α-helix	117	1
β-strand	118-121	4	1
α-helix	125-127	3

Chain C: 4 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	6
β-strand	16	1	5
β-strand	24-28	5	5
β-strand	33-35	3	12
β-strand	39-44	6	13
β-strand	47-50	4	6
α-helix	51-52	2
β-strand	55-60	6	5
α-helix	63-69	7
β-strand	71-74	4	13
β-strand	77-78	2	5
β-strand	87-92	6	13
β-strand	98-100	3	12
β-strand	105-113	9	5
β-strand	114	1	8
α-helix	117-118	2
β-strand	119-121	3	7
α-helix	125-127	3
β-strand	131	1	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
dUTP pyrophosphatase	A, B, C	protein	147	Homo sapiens	P33316 (AlphaFold model)

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

>1Q5H_1 dUTP pyrophosphatase (chains A, B, C)
HHHHHHMQLRFARLSEHATAPTRGSARAAGYDLYSAYDYTIPPMEKAVVKTDIQIALPSG
CYGRVAPRSGLAAKHFIDVGAGVIDEDYRGNVGVVLFNFGKEKFEVKKGDRIAQLICERI
FYPEIEEVQALDDTERGSGGFGSTGKN

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1
DUD	Deoxyuridine-5'-diphosphate	C9 H14 N2 O11 P2	3

Primary citation

Human dUTP pyrophosphatase: uracil recognition by a Beta hairpin and active sites formed by three separate subunits. Mol, C.D., Harris, J.M., McIntosh, E.M. et al. Structure (1996) 4:1077-1092. DOI 10.1016/S0969-2126(96)00114-1 · 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
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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