SMTL ID : 7oyf.1

Crystal structure of depupylase Dop in complex with Pup and ADP/trifluoromagnesate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

hetero-1-1-mer

Ligands

3 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 7 residues within 4Å: Chain A: E.8, Y.92, E.99 Ligands: MG.2, MG.3, ADP.4, KQB.17 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.8, A:Y.92, A:E.99 MG.2: 7 residues within 4Å: Chain A: E.10, Y.92, D.94, E.99 Chain B: E.28 Ligands: MG.1, KQB.17 5 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:E.10, A:D.94, A:E.99, B:E.28, H2O.8 MG.3: 6 residues within 4Å: Chain A: E.8, H.155, H.241 Ligands: MG.1, ADP.4, KQB.17 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.8, A:E.8, A:H.155, A:H.241

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.4: 23 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 Ligands: MG.1, MG.3, KQB.17 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:I.7, A:E.8, A:Y.92, A:S.101, A:T.102, A:P.230, A:R.433 Water bridges: A:R.90, A:R.90, A:R.90, A:R.90, A:Y.92, A:Y.92, A:R.239, A:R.239, A:H.241 Salt bridges: A:R.90, A:R.239, A:H.241 pi-Stacking: A:W.453 pi-Cation interactions: A:R.239

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

EDO.5: 1 residues within 4Å: Chain A: E.418 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.120, A:E.418 Water bridges: A:A.408 EDO.6: 1 residues within 4Å: Chain A: S.382 1 PLIP interactions: 1 interactions with chain A Water bridges: A:H.384 EDO.7: 4 residues within 4Å: Chain A: R.374, N.378, L.379, P.380 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.374, A:R.374 Water bridges: A:W.381 EDO.8: 5 residues within 4Å: Chain A: N.107, D.110, P.429, N.430, D.431 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.107, A:N.430, A:N.430 Water bridges: A:N.107, A:R.109 EDO.9: 2 residues within 4Å: Chain A: R.488, C.489 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.488, A:R.488 EDO.10: 3 residues within 4Å: Chain A: E.473, L.475, R.476 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.476 Water bridges: A:H.481 EDO.18: 1 residues within 4Å: Chain B: D.8 2 PLIP interactions: 2 interactions with chain B Water bridges: B:D.8, B:D.8

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

PEG.11: 4 residues within 4Å: Chain A: Y.255, D.334, M.335, D.338 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:M.335 PEG.12: 3 residues within 4Å: Chain A: E.210, G.284, R.287 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.287, A:R.287

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

ACT.13: 6 residues within 4Å: Chain A: D.459, R.463, D.464, S.465, L.466 Ligands: PGE.16 No protein-ligand interaction detected (PLIP)

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

PGE.14: 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 PGE.15: 4 residues within 4Å: Chain A: S.465, L.466, Q.467 Ligands: PGE.16 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.465, A:Q.467 Water bridges: A:R.468 PGE.16: 3 residues within 4Å: Chain A: L.466 Ligands: ACT.13, PGE.15 No protein-ligand interaction detected (PLIP)

1 x KQB: trifluoromagnesate monohydrate(Non-covalent)

KQB.17: 13 residues within 4Å: Chain A: E.8, E.10, Y.92, D.94, E.99, H.155, R.227, H.241 Chain B: E.28 Ligands: MG.1, MG.2, MG.3, ADP.4 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.28, A:Y.92 Metal complexes: B:E.28

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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