7DLV: Shrimp dUTPase

shrimp dUTPase in complex with Stl. Determined by X-ray diffraction at 2.52 Å resolution. Released 1 Dec 2021.

Method: X-ray diffraction
Resolution: 2.52 Å
Organisms: Penaeus vannamei, Staphylococcus aureus
Chains: 12
Atoms: 13,439
Mol. weight: 207.54 kDa
Ligands: CA
Released: 1 Dec 2021

Explore 7DLV in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7DLV contains 100 α-helices and 84 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: 6 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	71-76	6	1
β-strand	85	1	2
β-strand	94-97	4	2
α-helix	98	1
β-strand	102-104	3	3
β-strand	108-113	6	4
β-strand	116-119	4	1
α-helix	120-121	2
β-strand	124-129	6	2
α-helix	130-131	2
α-helix	132-138	7
β-strand	140-143	4	4
β-strand	146-147	2	2
β-strand	156-161	6	4
β-strand	167-169	3	3
α-helix	170	1
β-strand	174-182	9	2
β-strand	183-184	2	5
α-helix	186	1
β-strand	187-190	4	6

Chain B: 6 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	71-76	6	7
β-strand	85	1	8
β-strand	94-97	4	8
α-helix	98	1
β-strand	102-104	3	9
β-strand	108-113	6	10
β-strand	116-119	4	7
α-helix	120-121	2
β-strand	124-130	7	8
α-helix	131	1
α-helix	132-138	7
β-strand	140-143	4	10
β-strand	146-147	2	8
β-strand	156-161	6	10
β-strand	167-169	3	9
β-strand	174-182	9	8
β-strand	183-184	2	2
α-helix	186	1
β-strand	187-190	4	1
α-helix	194-195	2

Chains C and I: 5 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	71-76	6	6
β-strand	85	1	5
β-strand	94-97	4	5
β-strand	102-104	3	11
β-strand	108-113	6	12
β-strand	116-119	4	6
α-helix	120-121	2
β-strand	124-129	6	5
α-helix	130-131	2
α-helix	132-138	7
β-strand	140-143	4	12
β-strand	146-147	2	5
β-strand	156-161	6	12
β-strand	167-169	3	11
β-strand	174-182	9	5
β-strand	183-184	2	8
α-helix	186	1
β-strand	187-190	4	7
α-helix	194-195	2

Chains D, E and L: 11 helices, 0 β-strands

Element	Residues	Length
α-helix	14-24	11
α-helix	29-36	8
α-helix	40-48	9
α-helix	52-54	3
α-helix	55-65	11
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	141-151	11

Chain F: 10 helices, 0 β-strands

Element	Residues	Length
α-helix	14-24	11
α-helix	29-36	8
α-helix	40-48	9
α-helix	55-65	11
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	141-151	11

Chain G: 6 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	71-76	6	13
β-strand	85	1	14
β-strand	94-97	4	14
α-helix	98	1
β-strand	102-104	3	15
β-strand	108-113	6	16
β-strand	116-119	4	13
α-helix	120-121	2
β-strand	124-129	6	14
α-helix	130-131	2
α-helix	132-138	7
β-strand	140-143	4	16
β-strand	146-147	2	14
β-strand	156-161	6	16
β-strand	167-169	3	15
β-strand	174-182	9	14
β-strand	183-184	2	17
α-helix	186	1
β-strand	187-190	4	18
α-helix	194-195	2

Chain H: 6 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	71-76	6	19
β-strand	85	1	20
β-strand	94-97	4	20
α-helix	98	1
β-strand	102-104	3	21
β-strand	108-113	6	22
β-strand	116-119	4	19
α-helix	120-121	2
β-strand	124-130	7	20
α-helix	131	1
α-helix	132-138	7
β-strand	140-143	4	22
β-strand	146-147	2	20
β-strand	156-161	6	22
β-strand	167-169	3	21
α-helix	170	1
β-strand	174-182	9	20
β-strand	183-184	2	14
α-helix	186	1
β-strand	187-190	4	13

Chain J: 11 helices, 0 β-strands

Element	Residues	Length
α-helix	13-24	12
α-helix	29-36	8
α-helix	40-48	9
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	141-151	11

1 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
shrimp dUTPase	A, B, C, G, H, I	protein	149	Penaeus vannamei	A0A7S4XLZ3 (AlphaFold model)
Orf20	D, E, F, J, K, L	protein	157	Staphylococcus aureus	Q9F0J8 (AlphaFold model)

Sequence of entity 1 (A, B, C, G, H, I), FASTA

>7DLV_1 shrimp dUTPase (chains A, B, C, G, H, I)
SNAPGELKSVLRFKKLTEHAFTPSKGSKFAAGFDLCSAYDLVIPAVGKALVKTDIQVELP
EGCYGRIAPRSGLSWKHHIDVGAGVIDRDYRGNVGVVLFNHAKTDYEVKKGDRVAQLICE
KIIYPEIQEVEELMETERGEGGFGSTGNQ

Sequence of entity 2 (D, E, F, J, K, L), FASTA

>7DLV_2 Orf20 (chains D, E, F, J, K, L)
GAMEGAGQMAELPTHYGTIIKTLRKYMKLTQSKLSERTGFSQNTISNHENGNRNIGVNEI
EIYGKGLGIPSYILHRISDEFKEKGYSPTLNDFGKFDKMYSYVNKAYYNDGDIYYSSYDL
YDETIKLLELLKESKINVNDIDYDYVLKLYKQILSTD

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	2

Water and common crystallization additives (SO4) are not listed.

Primary citation

Structural basis of staphylococcal Stl inhibition on a eukaryotic dUTPase. Wang, F., Liu, C., Wang, C. et al. Int J Biol Macromol (2021) 184:821-830. DOI 10.1016/j.ijbiomac.2021.06.107 · PubMed

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