SMTL ID : 5ldb.1

Crystal Structure of Polyphosphate Kinase from Meiothermus ruber bound to ADP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

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

ADP.1: 15 residues within 4Å: Chain A: K.90, F.111, G.112, V.113, P.114, R.126, R.142, E.146, D.147, V.150, V.151, L.156, R.213, D.219 Ligands: MG.3 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:R.126, A:E.146, A:D.147, A:R.213, A:R.213 Water bridges: A:D.86, A:N.141, A:N.141, A:R.142, A:R.142, A:R.142, A:R.202 Salt bridges: A:K.90, A:R.142, A:R.213 ADP.5: 14 residues within 4Å: Chain B: K.90, F.111, G.112, V.113, P.114, R.126, R.142, E.146, D.147, V.150, V.151, L.156, D.219 Ligands: MG.7 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:R.126, B:E.146, B:D.147 Water bridges: B:N.141, B:N.141, B:R.202 Salt bridges: B:K.90, B:R.142 ADP.9: 14 residues within 4Å: Chain C: K.90, F.111, G.112, V.113, P.114, R.126, R.142, E.146, D.147, V.150, V.151, L.156, R.213, D.219 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:R.126, C:E.146, C:D.147 Water bridges: C:N.141, C:N.141 Salt bridges: C:K.90, C:R.142, C:R.213, C:R.213 ADP.11: 15 residues within 4Å: Chain D: K.90, F.111, G.112, V.113, P.114, R.126, R.142, E.146, D.147, V.150, V.151, L.156, R.213, D.219 Ligands: MG.13 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:R.126, D:E.146, D:D.147 Water bridges: D:N.141, D:N.141, D:R.213, D:R.213 Salt bridges: D:K.90, D:R.142, D:R.213

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

PO4.2: 6 residues within 4Å: Chain A: A.87, G.88, G.89, K.90, D.91, R.202 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:A.87, A:G.88, A:G.89, A:K.90, A:D.91 Water bridges: A:G.89, A:G.92, A:N.141, A:R.202, A:R.202 Salt bridges: A:K.90, A:R.202 PO4.6: 6 residues within 4Å: Chain B: A.87, G.88, G.89, K.90, D.91, R.202 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:A.87, B:G.88, B:G.89, B:K.90, B:D.91 Water bridges: B:G.92, B:R.202, B:R.202 Salt bridges: B:K.90, B:R.202 PO4.10: 6 residues within 4Å: Chain C: A.87, G.88, G.89, K.90, D.91, R.202 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:A.87, C:A.87, C:G.88, C:G.89, C:K.90, C:D.91 Water bridges: C:G.92, C:N.141 Salt bridges: C:K.90, C:R.202 PO4.12: 6 residues within 4Å: Chain D: A.87, G.88, G.89, K.90, D.91, R.202 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:A.87, D:G.88, D:G.89, D:K.90, D:D.91 Water bridges: D:G.92, D:G.92 Salt bridges: D:K.90, D:R.202

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain A: K.211 Ligands: ADP.1 No protein-ligand interaction detected (PLIP) MG.7: 3 residues within 4Å: Chain B: K.211, D.216 Ligands: ADP.5 No protein-ligand interaction detected (PLIP) MG.13: 2 residues within 4Å: Chain D: D.216 Ligands: ADP.11 No protein-ligand interaction detected (PLIP) MG.14: 4 residues within 4Å: Chain B: T.115, Q.117 Chain D: T.115, Q.117 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: B:T.115, D:T.115, H2O.11

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: G.92, R.95, N.252, R.255, N.256 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.95, A:N.252, A:R.255, A:R.255, A:N.256 Water bridges: A:G.89

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.8: 3 residues within 4Å: Chain B: K.49, N.252, W.253 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Parnell, A.E. et al., Substrate recognition and mechanism revealed by ligand-bound polyphosphate kinase 2 structures. Proc. Natl. Acad. Sci. U.S.A. (2018)

Release Date

2017-06-21

Peptides

Polyphosphate:AMP phosphotransferase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Polyphosphate:AMP phosphotransferase

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