SMTL ID : 7oy3.1

Crystal structure of depupylase Dop in complex with phosphorylated Pup and ADP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.78 Å

Oligo State

hetero-1-1-mer

Ligands

1 x K: POTASSIUM ION(Non-covalent)

K.1: 6 residues within 4Å: Chain A: E.8, H.155, H.241 Chain B: E.28 Ligands: MG.2, ADP.12 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.8, A:E.8, A:H.155, A:H.241

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 7 residues within 4Å: Chain A: E.8, Y.92, E.99 Chain B: E.28 Ligands: K.1, MG.3, ADP.12 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.8, A:Y.92, A:E.99 MG.3: 6 residues within 4Å: Chain A: E.10, Y.92, D.94, E.99 Chain B: E.28 Ligands: MG.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.10, A:D.94, A:E.99, H2O.18

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

EDO.4: 3 residues within 4Å: Chain A: V.407, A.408, E.418 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.418 Water bridges: A:A.408 EDO.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EDO.6: 5 residues within 4Å: Chain A: E.212, S.281, P.282, V.283, G.284 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.212, A:S.281, A:V.283, A:G.284 EDO.7: 6 residues within 4Å: Chain A: N.107, D.110, W.114, P.429, N.430, D.431 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.107, A:N.430, A:N.430 Water bridges: A:N.107, A:R.109, A:P.428 EDO.8: 2 residues within 4Å: Chain A: E.473, R.476 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.237, A:R.476 Water bridges: A:Y.237, A:E.473 EDO.9: 4 residues within 4Å: Chain A: R.374, N.378, L.379, P.380 No protein-ligand interaction detected (PLIP) EDO.10: 3 residues within 4Å: Chain A: G.271, F.272, S.274 4 PLIP interactions: 4 interactions with chain A Water bridges: A:G.271, A:G.271, A:F.272, A:S.274 EDO.11: 5 residues within 4Å: Chain A: G.199, F.200, P.293, E.371, W.381 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.200 Water bridges: A:E.371

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

ADP.12: 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 Chain B: E.28 Ligands: K.1, MG.2 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:I.7, A:I.7, A:Y.92, A:S.101, A:T.102, A:T.102, A:P.230, A:R.433 Water bridges: A:R.90, A:R.90, A:R.90, A:Y.92, A:Y.92, A:R.239, A:H.241, A:H.241 Salt bridges: A:R.90, A:R.239, A:H.241 pi-Cation interactions: A:R.239

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

ACT.13: 2 residues within 4Å: Chain A: Y.34, R.128 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.128 ACT.14: 3 residues within 4Å: Chain A: R.337, D.338, D.341 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:D.341 Hydrogen bonds: A:D.338, A:D.338, A:D.341 Water bridges: A:D.338, A:D.338

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

PEG.15: 5 residues within 4Å: Chain A: I.191, G.192, D.194, G.197, H.291 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.194, A:G.197

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

PGE.16: 8 residues within 4Å: Chain A: L.466, Q.467, R.468, V.469, P.470, L.499, T.500, E.503 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.466, A:R.468, A:L.499, A:E.503

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

Related Entries With Identical Sequence