SMTL ID : 7oxy.1

Crystal structure of depupylase Dop in complex with Pup and AMP-PCP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

hetero-1-1-mer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.1: 5 residues within 4Å: Chain A: E.10, D.94, E.99 Chain B: Q.28 Ligands: MG.4 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.10, A:D.94, A:E.99, H2O.1, H2O.2 MG.2: 5 residues within 4Å: Chain A: E.8, H.155, H.241 Ligands: MG.4, ACP.10 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.8, A:E.8, A:H.155, A:H.241, H2O.2 MG.3: 1 residues within 4Å: Ligands: ACP.10 No protein-ligand interaction detected (PLIP) MG.4: 6 residues within 4Å: Chain A: E.8, Y.92, E.99 Ligands: MG.1, MG.2, ACP.10 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.8, A:Y.92, A:E.99, H2O.2

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

EDO.5: 5 residues within 4Å: Chain A: R.109, D.110, P.429, N.430, D.431 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.107, A:R.109, A:N.430, A:N.430 Water bridges: A:P.428, A:D.431 EDO.6: 4 residues within 4Å: Chain A: D.94, H.95, T.218 Chain B: Q.28 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Water bridges: A:D.94, A:D.94, A:H.95, B:Q.28, B:Q.28 EDO.7: 2 residues within 4Å: Chain A: L.414, L.415 2 PLIP interactions: 2 interactions with chain A Water bridges: A:L.414, A:L.414 EDO.8: 4 residues within 4Å: Chain A: E.124, R.127, R.128, D.131 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.127, A:D.131 EDO.9: 3 residues within 4Å: Chain A: V.407, E.418, R.422 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.418, A:R.422 Water bridges: A:A.408

1 x ACP: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER(Non-covalent)

ACP.10: 24 residues within 4Å: Chain A: V.4, G.6, I.7, E.8, R.90, Y.92, E.99, S.101, T.102, P.103, E.104, N.157, Y.158, L.159, P.230, R.239, H.241, R.433, W.453, P.474 Chain B: Q.28 Ligands: MG.2, MG.3, MG.4 19 PLIP interactions: 18 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:I.7, A:E.8, A:S.101, A:T.102, A:T.102, A:R.227, A:P.230, A:R.239, A:R.239, A:R.433, B:Q.28 Water bridges: A:E.8, A:R.90, A:R.90, A:H.155 Salt bridges: A:R.90 pi-Stacking: A:W.453, A:W.453 pi-Cation interactions: A:R.239

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.11: 5 residues within 4Å: Chain A: D.459, R.463, D.464, L.466 Ligands: PEG.17 No protein-ligand interaction detected (PLIP) ACT.12: 4 residues within 4Å: Chain A: M.355, Q.356, S.358, R.359 No protein-ligand interaction detected (PLIP) ACT.13: 3 residues within 4Å: Chain A: R.337, D.338, D.341 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:D.341 Hydrogen bonds: A:D.338, A:D.338, A:D.341 ACT.14: 4 residues within 4Å: Chain A: Y.34, Q.44, R.128, H.426 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.44 Salt bridges: A:R.128

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

PEG.15: 4 residues within 4Å: Chain A: R.109, Y.255, M.335, D.338 1 PLIP interactions: 1 interactions with chain A Water bridges: A:M.335 PEG.16: 3 residues within 4Å: Chain A: E.210, V.283, R.287 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.287, A:R.287 PEG.17: 3 residues within 4Å: Chain A: L.466 Ligands: ACT.11, PGE.18 No protein-ligand interaction detected (PLIP)

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

PGE.18: 3 residues within 4Å: Chain A: S.465, L.466 Ligands: PEG.17 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.465, A:L.466 PGE.19: 8 residues within 4Å: Chain A: I.191, G.199, F.200, H.291, P.293, L.367, E.371, W.381 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.200, A:H.291

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
Prokaryotic ubiquitin-like protein Pup: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Depupylase

Prokaryotic ubiquitin-like protein Pup

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