SMTL ID : 7pwj.1

dUTPase from human in complex with Stl

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.94 Å

Oligo State

hetero-3-3-mer

Ligands

20 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 1 residues within 4Å: Chain A: R.35 Ligand excluded by PLIP EDO.2: 3 residues within 4Å: Chain A: T.28, S.30, K.31 Ligand excluded by PLIP EDO.3: 3 residues within 4Å: Chain A: Y.100, D.140, Y.141 Ligand excluded by PLIP EDO.6: 2 residues within 4Å: Chain B: S.57 Ligands: EDO.9 Ligand excluded by PLIP EDO.7: 3 residues within 4Å: Chain B: L.12, S.13, E.14 Ligand excluded by PLIP EDO.8: 3 residues within 4Å: Chain B: V.126, Q.127, A.128 Ligand excluded by PLIP EDO.9: 5 residues within 4Å: Chain B: G.4, M.5, Q.6, S.57 Ligands: EDO.6 Ligand excluded by PLIP EDO.12: 6 residues within 4Å: Chain C: D.30, R.66, S.67, R.109, Q.112 Chain E: Y.105 Ligand excluded by PLIP EDO.14: 4 residues within 4Å: Chain C: G.98, K.99, E.100 Chain D: K.44 Ligand excluded by PLIP EDO.15: 6 residues within 4Å: Chain C: G.68, L.69, H.73 Chain E: S.114, S.115, Y.116 Ligand excluded by PLIP EDO.16: 3 residues within 4Å: Chain C: V.126, Q.127, A.128 Ligand excluded by PLIP EDO.20: 5 residues within 4Å: Chain D: L.69, K.72, H.73 Chain F: Y.116, D.155 Ligand excluded by PLIP EDO.21: 3 residues within 4Å: Chain B: A.128 Chain D: L.12, Q.52 Ligand excluded by PLIP EDO.22: 2 residues within 4Å: Chain D: V.126, Q.127 Ligand excluded by PLIP EDO.23: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP EDO.25: 5 residues within 4Å: Chain B: G.138 Chain E: Y.24, G.92, D.95, K.96 Ligand excluded by PLIP EDO.26: 2 residues within 4Å: Chain E: K.31, R.35 Ligand excluded by PLIP EDO.27: 6 residues within 4Å: Chain B: G.88, N.89 Chain F: N.107, D.108, G.109 Ligands: GOL.10 Ligand excluded by PLIP EDO.31: 1 residues within 4Å: Chain F: R.35 Ligand excluded by PLIP EDO.32: 2 residues within 4Å: Chain F: R.51, N.52 Ligand excluded by PLIP

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 6 residues within 4Å: Chain A: H.73, D.77 Chain B: R.11, A.16, T.17, A.18 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:A.18 Salt bridges: B:R.11, A:H.73 SO4.5: 6 residues within 4Å: Chain B: D.76, V.77 Chain C: D.76, V.77 Chain D: D.76, V.77 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:V.77, D:D.76 SO4.17: 4 residues within 4Å: Chain C: R.11, T.17, A.18 Chain E: H.73 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain E Hydrogen bonds: C:A.18 Water bridges: C:A.18 Salt bridges: C:R.11, E:H.73 SO4.18: 5 residues within 4Å: Chain D: R.11, T.17, A.18 Chain F: H.73, K.80 7 PLIP interactions: 4 interactions with chain F, 3 interactions with chain D Water bridges: F:Y.14, F:H.73, D:R.11 Salt bridges: F:H.73, F:K.80, D:R.11 Hydrogen bonds: D:A.18 SO4.24: 2 residues within 4Å: Chain E: T.28, K.31 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:T.28 Salt bridges: E:K.31 SO4.28: 2 residues within 4Å: Chain F: N.135, N.137 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:N.135, F:N.135, F:N.137

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 4 residues within 4Å: Chain B: K.48, N.89 Chain F: G.109 Ligands: EDO.27 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain F Hydrogen bonds: B:K.48, B:K.48, B:N.89, F:G.109 GOL.11: 3 residues within 4Å: Chain B: R.117 Chain C: R.117 Chain D: R.117 5 PLIP interactions: 1 interactions with chain D, 2 interactions with chain B, 2 interactions with chain C Hydrogen bonds: D:R.117, B:R.117, B:R.117, C:R.117, C:R.117 GOL.13: 5 residues within 4Å: Chain A: D.108, G.109 Chain C: L.12, K.48, N.89 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:G.109, C:K.48, C:N.89, C:N.89 GOL.19: 5 residues within 4Å: Chain D: L.12, K.48, N.89 Chain E: G.109, D.110 7 PLIP interactions: 4 interactions with chain D, 3 interactions with chain E Hydrogen bonds: D:K.48, D:N.89, E:G.109, E:D.110, E:D.110 Water bridges: D:N.89, D:N.89 GOL.29: 4 residues within 4Å: Chain F: R.22, K.23, T.28, Q.29 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:R.22, F:R.22, F:Q.29 GOL.30: 7 residues within 4Å: Chain F: P.11, T.12, H.13, Y.14, G.15, T.16, G.49 8 PLIP interactions: 8 interactions with chain F Hydrogen bonds: F:T.12, F:H.13, F:Y.14, F:G.15, F:T.16, F:T.16, F:T.16 Water bridges: F:T.12

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sanz-Frasquet, C. et al., The Bacteriophage-Phage-Inducible Chromosomal Island Arms Race Designs an Interkingdom Inhibitor of dUTPases. Microbiol Spectr (2023)

Release Date

2022-12-28

Peptides

Orf20: AEF
Deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial: BCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
CCC

E
EEE

F
FFF

B
AAA

C
BBB

D
DDD

Orf20

Deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial