9TRU: Zebrafish dUTPase

Zebrafish dUTPase in complex with staphylococcal Stl repressor. Determined by X-ray diffraction at 2.26 Å resolution. Released 23 Sept 2026.

Method: X-ray diffraction
Resolution: 2.26 Å
Organisms: Danio rerio, Staphylococcus aureus
Chains: 12
Atoms: 13,671
Mol. weight: 229.74 kDa
Ligands: MG
Released: 23 Sept 2026

Explore 9TRU in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9TRU contains 99 α-helices and 87 β-strands across 12 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: 5 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	26-31	6	1
β-strand	40	1	2
β-strand	49-52	4	2
β-strand	57-59	3	3
α-helix	60	1
β-strand	63-68	6	4
β-strand	71-74	4	1
α-helix	75-76	2
β-strand	79-84	6	2
α-helix	87-93	7
β-strand	95-98	4	4
β-strand	101-102	2	2
β-strand	111-116	6	4
β-strand	122-124	3	3
β-strand	129-137	9	2
β-strand	138	1	5
α-helix	141	1
β-strand	142-146	5	6
α-helix	149-152	4

Chain B: 4 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	26-31	6	7
β-strand	40	1	8
β-strand	48-52	5	8
β-strand	57-59	3	9
α-helix	60	1
β-strand	63-68	6	10
β-strand	71-74	4	7
α-helix	75-76	2
β-strand	79-84	6	8
α-helix	87-93	7
β-strand	95-98	4	10
β-strand	101-102	2	8
β-strand	111-116	6	10
β-strand	122-124	3	9
β-strand	129-137	9	8
β-strand	138	1	2
α-helix	141	1
β-strand	142-145	4	1

Chain C: 4 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	26-31	6	6
β-strand	40	1	5
β-strand	49-52	4	5
β-strand	57-59	3	11
α-helix	60	1
β-strand	63-68	6	12
β-strand	71-74	4	6
α-helix	75-76	2
β-strand	79-84	6	5
α-helix	87-93	7
β-strand	95-98	4	12
β-strand	101-102	2	5
β-strand	111-116	6	12
β-strand	122-124	3	11
β-strand	129-137	9	5
β-strand	138	1	8
α-helix	141	1
β-strand	142-146	5	7

Chains D and F: 5 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	26-31	6	13
β-strand	40	1	14
β-strand	48-52	5	14
β-strand	57-59	3	15
α-helix	60	1
β-strand	63-68	6	16
β-strand	71-74	4	13
α-helix	75-76	2
β-strand	79-84	6	14
α-helix	87-93	7
β-strand	95-98	4	16
β-strand	101-102	2	14
β-strand	111-116	6	16
β-strand	122-124	3	15
β-strand	129-137	9	14
β-strand	138	1	17
α-helix	141	1
β-strand	142-145	4	18
α-helix	149-151	3

Chain E: 4 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	26-31	6	19
β-strand	40	1	20
β-strand	49-52	4	20
β-strand	57-59	3	21
α-helix	60	1
β-strand	63-68	6	22
β-strand	71-74	4	19
α-helix	75-76	2
β-strand	79-84	6	20
α-helix	87-93	7
β-strand	95-98	4	22
β-strand	101-102	2	20
β-strand	111-116	6	22
β-strand	122-124	3	21
β-strand	129-137	9	20
β-strand	138	1	14
α-helix	141	1
β-strand	142-145	4	13

Chain G: 12 helices, 1 β-strand

Element	Residues	Length	Sheet
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
β-strand	84	1	9
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	141-152	12

Chain H: 12 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	9	1	25
α-helix	13-24	12
α-helix	29-36	8
α-helix	40-47	8
α-helix	52-53	2
β-strand	54	1	25
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	141-152	12

Chain I: 12 helices, 0 β-strands

Element	Residues	Length
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	118-132	15
α-helix	136-138	3
α-helix	141-152	12

2 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Deoxyuridine 5'-triphosphate nucleotidohydrolase	A, B, C, D, E, F	protein	186	Danio rerio	Q5XJ23 (AlphaFold model)
Orf20	G, H, I, J, K, L	protein	156	Staphylococcus aureus	Q9F0J8 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F), FASTA

>9TRU_1 Deoxyuridine 5'-triphosphate nucleotidohydrolase (chains A, B, C, D, E, F)
MGSSHHHHHHSSGLVPRGSHMSEVTEAVSPHKRAKSDAVNGAEERAVLKFAKLTEHATTP
SRGSNRAAGYDLYSAYDYSIGPMDKTLVKTGIQIAVPHGYYGRVAPRSGLAVKHFVDVGA
GVVDEDYRGNLGVVIFNFNKEPFEVKKGDRIAQLICEKICYPDLQELQTLDETERGAGGF
GSTGTN

Sequence of entity 2 (G, H, I, J, K, L), FASTA

>9TRU_2 Orf20 (chains G, H, I, J, K, L)
MEGAGQMAELPTHYGTIIKTLRKYMKLTQSKLSERTGFSQNTISNHENGNRNIGVNEIEI
YGKGLGIPSYILHRISDEFKEKGYSPTLNDFGKFDKMYSYVNKAYYNDGDIYYSSYDLYD
ETIKLLELLKESKINVNDIDYDYVLKLYKQILSTDT

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2

Primary citation

A bacterial protein inhibitor of dUTPase disrupts zebrafish embryogenesis through a conserved active-site mechanism. Perey-Simon, V., Toth, Z.S., Dombovari, D. et al. Protein Sci (2026) 35:e70767-e70767. DOI 10.1002/pro.70767 · PubMed

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