SMTL ID : 7nmj.2 (1 other biounit)

Crystal structure of Polyphosphate Kinase 2 from Deinococcus radiodurans in complex with ADP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.08 Å

Oligo State

homo-dimer

Ligands

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

ADP.1: 13 residues within 4Å: Chain A: K.70, F.91, K.92, Q.93, P.94, R.106, R.122, E.126, D.127, V.130, T.131, M.136 Ligands: GOL.2 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:R.106, A:E.126, A:D.127 Water bridges: A:R.106, A:D.127, A:N.193 Salt bridges: A:K.70, A:K.92, A:K.92, A:R.122 ADP.4: 15 residues within 4Å: Chain B: K.70, S.90, F.91, K.92, Q.93, P.94, R.106, R.122, E.126, D.127, V.130, T.131, M.136, N.193 Ligands: ADP.5 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:R.106, B:D.127 Water bridges: B:D.66, B:D.66, B:K.92, B:R.106 Salt bridges: B:K.70, B:K.92, B:R.122, B:R.122 ADP.5: 17 residues within 4Å: Chain B: R.65, D.66, A.67, A.68, G.69, K.70, D.71, G.72, N.121, A.181, R.182, N.185, K.188, K.191, K.231, R.234 Ligands: ADP.4 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:R.65, B:A.67, B:A.68, B:G.69, B:K.70, B:D.71, B:G.72, B:K.188, B:K.191, B:K.231, B:R.234, B:R.234 Salt bridges: B:K.70, B:R.182 pi-Cation interactions: B:K.188, B:K.231

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 10 residues within 4Å: Chain A: D.66, A.67, A.68, G.69, K.70, D.71, G.72, R.182 Ligands: ADP.1, GOL.3 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:A.67, A:G.69, A:K.70, A:K.70, A:D.71, A:D.71, A:D.71, A:G.72 GOL.3: 5 residues within 4Å: Chain A: R.182, K.188, K.191, K.231 Ligands: GOL.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.182, A:R.182, A:K.188, A:K.191

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Silva, S.T.N. et al., Crystal structure of Polyphosphate Kinase 2 from Deinococcus radiodurans in complex with ADP. To Be Published

Release Date

2021-04-07

Peptides

PPK2 domain-containing protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

PPK2 domain-containing protein

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