SMTL ID : 7oyh.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

hetero-1-1-mer

Ligands

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

MG.1: 7 residues within 4Å: Chain A: E.8, Y.92, E.99, S.101 Ligands: MG.2, ADP.5, MG.28 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.8, A:Y.92, A:E.99, H2O.1 MG.2: 6 residues within 4Å: Chain A: E.10, D.94, E.99 Chain B: E.28 Ligands: MG.1, MG.28 6 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:E.10, A:D.94, A:E.99, B:E.28, H2O.1, H2O.9 MG.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.4: 1 residues within 4Å: Ligands: MF4.27 No protein-ligand interaction detected (PLIP) MG.28: 8 residues within 4Å: Chain A: E.8, Y.92, D.94 Chain B: E.28 Ligands: MG.1, MG.2, ADP.5, MF4.27 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.28, H2O.1, H2O.2, H2O.14

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

ADP.5: 22 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, L.159, P.230, R.239, R.433, W.453, P.474 Ligands: MG.1, PGE.24, MF4.27, MG.28 17 PLIP interactions: 16 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:I.7, A:E.8, A:R.90, A:Y.92, A:S.101, A:T.102, A:P.230, A:R.433 Water bridges: A:Y.92, A:Y.92, A:R.239, A:R.239, B:E.28 Salt bridges: A:R.90, A:R.239 pi-Stacking: A:W.453 pi-Cation interactions: A:R.239

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

EDO.6: 3 residues within 4Å: Chain A: V.407, A.408, E.418 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.120, A:R.120, A:R.120, A:A.408, A:E.418 EDO.7: 6 residues within 4Å: Chain A: R.109, D.110, W.114, P.429, N.430, D.431 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.107, A:R.109, A:N.430 Water bridges: A:P.428 EDO.8: 2 residues within 4Å: Chain A: R.488, E.494 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.488 EDO.9: 3 residues within 4Å: Chain A: E.473, L.475, R.476 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.476 EDO.10: 2 residues within 4Å: Chain A: D.168, R.171 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.168, A:R.171 EDO.11: 5 residues within 4Å: Chain A: G.192, A.193, D.194, D.207, R.287 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.193, A:D.194, A:D.194, A:R.287, A:R.287 EDO.12: 4 residues within 4Å: Chain A: N.430, Y.435, R.439, R.479 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.435, A:R.479 EDO.13: 3 residues within 4Å: Chain A: A.383, H.384, K.385 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.384, A:K.385 Water bridges: A:S.382 EDO.14: 3 residues within 4Å: Chain A: E.280, S.281, H.302 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.281 EDO.15: 2 residues within 4Å: Chain A: R.439, K.443 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.439 EDO.29: 2 residues within 4Å: Chain B: D.8, D.9 1 PLIP interactions: 1 interactions with chain B Water bridges: B:D.9 EDO.30: 3 residues within 4Å: Chain A: H.384 Chain B: A.15, E.16 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.15, B:E.16 Water bridges: B:E.17

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

PEG.16: 4 residues within 4Å: Chain A: Y.255, D.334, M.335, D.338 1 PLIP interactions: 1 interactions with chain A Water bridges: A:M.335 PEG.17: 5 residues within 4Å: Chain A: Q.467, R.468, L.499, E.503 Ligands: PEG.19 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.467, A:E.503 PEG.18: 2 residues within 4Å: Chain A: L.466 Ligands: PEG.19 No protein-ligand interaction detected (PLIP) PEG.19: 6 residues within 4Å: Chain A: S.465, L.466, Q.467, R.468 Ligands: PEG.17, PEG.18 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.465, A:R.468, A:R.468

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

ACT.20: 5 residues within 4Å: Chain A: D.459, R.463, D.464, S.465, L.466 No protein-ligand interaction detected (PLIP) ACT.21: 4 residues within 4Å: Chain A: S.281, P.282, V.283, G.284 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.281, A:V.283, A:G.284 ACT.22: 3 residues within 4Å: Chain A: R.463, D.464, S.465 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:D.464 Hydrogen bonds: A:D.464, A:S.465 Salt bridges: A:R.463

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

PGE.23: 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.24: 5 residues within 4Å: Chain A: W.47, F.49, R.90, H.231 Ligands: ADP.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.90, A:R.90

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

SO4.25: 3 residues within 4Å: Chain A: V.211, E.212, V.213 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.212, A:V.213 Water bridges: A:E.212, A:V.213 SO4.26: 5 residues within 4Å: Chain A: E.198, R.374, L.379, P.380, W.381 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.198, A:W.381 Salt bridges: A:R.374

1 x MF4: TETRAFLUOROMAGNESATE(2-)(Non-covalent)

MF4.27: 9 residues within 4Å: Chain A: T.217, R.227, E.229, R.239, H.241 Chain B: E.28 Ligands: MG.4, ADP.5, MG.28 No protein-ligand interaction detected (PLIP)

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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