SMTL ID : 4b0t.1

Structure of the Pup Ligase PafA of the Prokaryotic Ubiquitin-like Modification Pathway in Complex with ADP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.16 Å

Oligo State

homo-dimer

Ligands

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

ADP.1: 24 residues within 4Å: Chain A: R.60, A.72, T.73, A.74, E.75, N.132, Y.133, L.134, D.208, P.210, H.211, A.212, R.219, R.418, W.440, P.458 Chain B: I.12, G.14, I.15, E.16, K.444, N.446, P.450 Ligands: MG.2 18 PLIP interactions: 13 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:T.73, A:T.73, A:N.132, A:H.211, A:R.219, A:R.418, B:N.446 Water bridges: A:R.60, B:K.444, B:K.444 Salt bridges: A:R.60, A:H.211, A:H.211, A:R.219, A:R.219, B:K.444, B:K.444 pi-Cation interactions: A:R.219 ADP.3: 20 residues within 4Å: Chain A: I.12, G.14, I.15, E.16 Chain B: R.60, A.72, T.73, A.74, E.75, N.132, Y.133, L.134, P.210, H.211, A.212, R.219, R.418, W.440, P.458 Ligands: MG.4 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:T.73, B:T.73, B:N.132, B:H.211, B:R.219, B:R.418 Water bridges: B:N.52, B:N.52, B:N.52, B:R.60, B:R.219, B:R.219 Salt bridges: B:R.60, B:H.211, B:R.219 pi-Cation interactions: B:R.219, B:R.219

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: R.60 Chain B: E.16 Ligands: ADP.1 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:E.16, H2O.53, H2O.63, H2O.250, H2O.251 MG.4: 3 residues within 4Å: Chain A: E.16 Chain B: R.60 Ligands: ADP.3 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.16, H2O.16, H2O.17, H2O.18, H2O.235

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ozcelik, D. et al., Structures of Pup Ligase Pafa and Depupylase Dop from the Prokaryotic Ubiquitin-Like Modification Pathway. Nat.Commun. (2012)

Release Date

2012-09-12

Peptides

PUP--PROTEIN LIGASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

PUP--PROTEIN LIGASE