SMTL ID : 5lrt.1

Structure of the Deamidase-Depupylase Dop of the Prokaryotic Ubiquitin-like Modification Pathway in Complex with ADP and Phosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

monomer

Ligands

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

ADP.1: 27 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, R.227, E.229, P.230, H.231, R.239, H.241, R.433, W.453, P.474 Ligands: MG.2, MG.3, MG.4, PO4.6 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:I.7, A:S.101, 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:Y.92 Salt bridges: A:R.90, A:R.227, A:R.239, A:R.239, A:H.241 pi-Cation interactions: A:R.239

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: E.229, R.239 Ligands: ADP.1 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.229, H2O.1, H2O.2, H2O.4, H2O.7 MG.3: 7 residues within 4Å: Chain A: E.8, Y.92, E.99 Ligands: ADP.1, MG.4, MG.5, PO4.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.8, A:Y.92, A:E.99 MG.4: 7 residues within 4Å: Chain A: E.8, H.155, R.227, H.241 Ligands: ADP.1, MG.3, PO4.6 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.8, A:E.8, A:H.155, A:H.241 MG.5: 7 residues within 4Å: Chain A: E.10, Y.92, D.94, E.99 Ligands: MG.3, PO4.6, NA.11 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.10, A:D.94, A:E.99, H2O.6

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.6: 13 residues within 4Å: Chain A: E.8, E.10, Y.92, D.94, E.99, H.155, R.227, H.241 Ligands: ADP.1, MG.3, MG.4, MG.5, NA.11 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Y.92 Water bridges: A:Y.92, A:Y.92, A:R.227, A:R.227 Salt bridges: A:H.155, A:R.227, A:H.241

1 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)

P6G.7: 9 residues within 4Å: Chain A: S.358, R.359, A.365, S.368, I.369, L.402, L.406, R.409, R.411 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.358, A:R.411, A:R.411 Water bridges: A:R.405

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

PGE.8: 6 residues within 4Å: Chain A: L.113, A.420, T.423, E.427, P.428, N.430 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.430 PGE.9: 5 residues within 4Å: Chain A: R.109, Y.255, M.335, D.338, L.415 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.109, A:L.415

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

PEG.10: 3 residues within 4Å: Chain A: R.120, P.398, E.418 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.120, A:R.127, A:E.418

1 x NA: SODIUM ION(Non-functional Binders)

NA.11: 6 residues within 4Å: Chain A: E.10, D.94, T.217, T.218 Ligands: MG.5, PO4.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.217, A:T.217

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bolten, M. et al., Depupylase Dop Requires Inorganic Phosphate in the Active Site for Catalysis. J. Biol. Chem. (2017)

Release Date

2017-02-01

Peptides

Depupylase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Depupylase

Related Entries With Identical Sequence