SMTL ID : 7oxv.1

Crystal structure of depupylase Dop in the Dop-loop-inserted state

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.39 Å

Oligo State

monomer

Ligands

4 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.1: 5 residues within 4Å: Chain A: I.369, L.402, L.406, R.409, R.411 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.411, A:R.411 Water bridges: A:R.405 PGE.2: 7 residues within 4Å: Chain A: D.338, D.341, R.342, T.345, T.346, R.349, D.360 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.342 PGE.3: 8 residues within 4Å: Chain A: H.2, R.3, N.161, A.266, E.269, D.270, Y.323, R.327 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.3, A:R.3, A:N.161, A:E.269, A:Y.323, A:R.327 PGE.4: 5 residues within 4Å: Chain A: D.341, E.344, T.345, V.348, R.349 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.341, A:T.345, A:R.349

1 x SCN: THIOCYANATE ION(Non-functional Binders)

SCN.5: 7 residues within 4Å: Chain A: W.47, N.157, Y.158, L.159, P.230, H.231, R.239 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.231

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.6: 7 residues within 4Å: Chain A: L.113, W.114, A.420, T.423, E.427, P.428, N.430 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.423, A:P.428, A:N.430 Water bridges: A:N.430 PEG.7: 3 residues within 4Å: Chain A: V.348, D.352, Q.356 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.356, A:Q.356

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

EDO.8: 6 residues within 4Å: Chain A: G.88, A.89, R.90, S.101, T.102, P.103 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:W.47, A:G.88, A:S.101 Water bridges: A:L.85, A:R.437

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cui, H. et al., Structures of prokaryotic ubiquitin-like protein Pup in complex with depupylase Dop reveal the mechanism of catalytic phosphate formation. Nat Commun (2021)

Release Date

2021-12-01

Peptides

Depupylase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Depupylase

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