SMTL ID : 6dzg.1

Crystal structure of polyphosphate kinase 2 class I (SMc02148) in complex with ADP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.87 Å

Oligo State

homo-tetramer

Ligands

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

ADP.1: 11 residues within 4Å: Chain A: K.97, T.119, K.120, R.149, N.153, V.157, F.163, S.220, M.222 Chain B: N.109, R.111 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.153, A:S.220 Water bridges: A:K.120, A:R.133 Salt bridges: A:K.97, A:R.149, B:R.111 pi-Stacking: A:F.163 ADP.3: 11 residues within 4Å: Chain A: N.109, R.111 Chain B: T.119, K.120, P.121, R.149, N.153, V.157, F.163, S.220, M.222 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:N.153, B:N.153, B:S.220, B:S.220, A:N.109 Water bridges: B:K.120, B:R.133 Salt bridges: B:R.149, A:R.111 pi-Stacking: B:F.163 ADP.6: 10 residues within 4Å: Chain C: T.119, K.120, R.149, N.153, V.157, F.163, S.220, M.222 Chain D: N.109, R.111 8 PLIP interactions: 2 interactions with chain D, 6 interactions with chain C Hydrogen bonds: D:N.109, C:N.153, C:S.220, C:S.220 Salt bridges: D:R.111 Water bridges: C:K.120, C:R.133 pi-Stacking: C:F.163

5 x MLT: D-MALATE(Non-covalent)

MLT.2: 8 residues within 4Å: Chain A: A.94, A.95, G.96, K.97, G.98, G.99, R.209, K.218 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:K.218 Hydrogen bonds: A:A.95, A:G.96, A:K.97, A:K.97, A:G.98, A:G.99 Salt bridges: A:K.97, A:R.209, A:R.209, A:K.218 MLT.4: 8 residues within 4Å: Chain B: A.94, A.95, G.96, K.97, G.98, G.99, R.209, K.218 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:K.218 Hydrogen bonds: B:A.94, B:A.95, B:G.96, B:K.97, B:G.98, B:G.99 Water bridges: B:K.259, B:K.259 Salt bridges: B:K.97, B:R.209, B:R.209, B:K.218, B:K.259 MLT.5: 5 residues within 4Å: Chain B: E.59, T.63, R.261, I.264, R.268 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.59, B:T.63 Salt bridges: B:R.261, B:R.268 MLT.7: 8 residues within 4Å: Chain C: A.94, A.95, G.96, K.97, G.98, G.99, R.209, K.218 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:A.94, C:A.95, C:G.96, C:K.97, C:K.97, C:K.97, C:G.98, C:G.99 Salt bridges: C:K.97, C:R.209, C:R.209, C:K.218, C:K.259 MLT.9: 8 residues within 4Å: Chain D: A.94, A.95, G.96, K.97, G.98, G.99, R.209, K.218 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:K.218 Hydrogen bonds: D:A.94, D:A.95, D:G.96, D:K.97, D:G.98, D:G.99 Salt bridges: D:K.97, D:R.209, D:R.209, D:K.218

1 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.8: 10 residues within 4Å: Chain C: R.111 Chain D: T.119, K.120, R.149, N.153, V.157, F.163, S.220, M.222, D.223 12 PLIP interactions: 3 interactions with chain C, 9 interactions with chain D Water bridges: C:N.109, C:R.111, C:R.111, D:K.120, D:R.133 Hydrogen bonds: D:L.118, D:R.149, D:N.153, D:S.220, D:D.223 Salt bridges: D:R.149 pi-Stacking: D:F.163

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nocek, B. et al., Structural insights into substrate selectivity and activity ofbacterial polyphosphate kinases. To Be Published

Release Date

2019-07-10

Peptides

Polyphosphate:ADP phosphotransferase 1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Polyphosphate:ADP phosphotransferase 1