SMTL ID : 4bjr.1

Crystal structure of the complex between Prokaryotic Ubiquitin-like Protein Pup and its Ligase PafA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-dimer

Ligands

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 21 residues within 4Å: Chain A: I.14, G.16, I.17, E.18, R.62, Y.64, E.72, A.74, T.75, A.76, E.77, N.134, L.136, P.212, H.213, A.214, R.221, R.420, W.442, P.460 Ligands: MG.2 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:I.17, A:E.72, A:T.75, A:T.75, A:E.77, A:N.134, A:H.213, A:R.221, A:R.420 Water bridges: A:R.62 Salt bridges: A:R.62, A:R.62 pi-Stacking: A:W.442 pi-Cation interactions: A:R.221 ATP.3: 24 residues within 4Å: Chain A: E.517 Chain B: I.14, G.16, I.17, E.18, R.62, Y.64, E.72, A.74, T.75, A.76, E.77, N.134, Y.135, L.136, P.212, H.213, A.214, R.221, R.420, W.442, P.460 Ligands: MG.4, MG.5 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:I.17, B:R.62, B:Y.64, B:E.72, B:T.75, B:T.75, B:T.75, B:N.134, B:H.213, B:R.221, B:R.420 Water bridges: B:R.221, B:R.221 Salt bridges: B:R.62, B:R.62, B:H.213, B:R.221 pi-Stacking: B:W.442 pi-Cation interactions: B:R.221

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: E.18, Y.64, E.72 Ligands: ATP.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.18, A:Y.64, A:E.72 MG.4: 5 residues within 4Å: Chain B: E.18, Y.64, E.72 Ligands: ATP.3, MG.5 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.18, B:Y.64, B:E.72 MG.5: 4 residues within 4Å: Chain B: E.18, H.223 Ligands: ATP.3, MG.4 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.18, H2O.3

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Barandun, J. et al., Crystal Structure of the Complex between Prokaryotic Ubiquitin-Like Protein Pup and its Ligase Pafa. J.Am.Chem.Soc. (2013)

Release Date

2013-05-01

Peptides

PUP--PROTEIN LIGASE, PROKARYOTIC UBIQUITIN-LIKE PROTEIN PUP: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

PUP--PROTEIN LIGASE, PROKARYOTIC UBIQUITIN-LIKE PROTEIN PUP