SMTL ID : 3rhf.2 (2 other biounits)

Crystal structure of Polyphosphate Kinase 2 from Arthrobacter aurescens TC1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

homo-tetramer

Ligands

4 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.1: 5 residues within 4Å: Chain A: F.277, E.282 Chain C: Y.210, S.211, R.212 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.212 PGE.2: 9 residues within 4Å: Chain A: A.17, T.180, I.181, E.238, I.239, P.241, H.243, L.260, A.264 No protein-ligand interaction detected (PLIP) PGE.19: 9 residues within 4Å: Chain D: A.17, T.180, I.181, V.182, I.239, P.241, L.260, D.263, A.264 No protein-ligand interaction detected (PLIP) PGE.22: 6 residues within 4Å: Chain D: K.43, K.47, K.249, K.250, W.251, R.254 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:K.43, D:K.47, D:R.254, D:R.254 Water bridges: D:W.251

4 x FLC: CITRATE ANION(Non-covalent)

FLC.3: 5 residues within 4Å: Chain A: K.43, K.47, K.250, W.251, R.254 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:K.43, A:K.250 Hydrogen bonds: A:K.47, A:K.47, A:K.250, A:W.251, A:R.254, A:R.254 Salt bridges: A:K.43, A:K.47, A:K.47, A:K.250, A:R.254 FLC.7: 10 residues within 4Å: Chain B: M.83, D.84, T.85, A.86, G.87, K.88, G.89, D.139, R.200 Chain D: Q.102 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:K.88 Hydrogen bonds: B:T.85, B:A.86, B:G.87, B:K.88, B:G.89, D:Q.102 Salt bridges: B:K.88, B:K.88, B:K.110, B:R.140, B:R.200 FLC.14: 9 residues within 4Å: Chain A: Q.102 Chain C: D.84, T.85, K.88, G.89, K.110, D.139, R.140, R.200 20 PLIP interactions: 20 interactions with chain C Hydrogen bonds: C:D.84, C:T.85, C:K.88, C:K.88, C:G.89, C:R.140, C:R.140 Water bridges: C:G.87, C:G.87, C:G.87, C:G.87, C:G.90, C:K.110, C:R.200 Salt bridges: C:K.88, C:K.88, C:K.88, C:K.110, C:R.140, C:R.200 FLC.20: 9 residues within 4Å: Chain B: Q.102 Chain D: D.84, T.85, K.88, G.89, K.110, D.139, R.140, R.200 23 PLIP interactions: 22 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:D.84, D:T.85, D:K.88, D:K.88, D:K.88, D:G.89, D:R.140, D:R.140, B:Q.102 Water bridges: D:D.84, D:G.87, D:G.87, D:K.88, D:G.90, D:G.90, D:K.110, D:R.200, D:R.200 Salt bridges: D:K.88, D:K.88, D:K.110, D:R.140, D:R.200

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

PO4.4: 4 residues within 4Å: Chain A: R.200, K.206, K.209, K.250 6 PLIP interactions: 6 interactions with chain A Water bridges: A:K.206, A:K.206 Salt bridges: A:R.200, A:K.206, A:K.209, A:K.250 PO4.5: 7 residues within 4Å: Chain A: M.83, D.84, T.85, A.86, G.87, K.88, G.89 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:D.84, A:T.85, A:T.85, A:A.86, A:G.87, A:K.88, A:G.89 Water bridges: A:G.90 Salt bridges: A:K.88 PO4.9: 4 residues within 4Å: Chain B: R.200, K.206, K.209, K.250 5 PLIP interactions: 5 interactions with chain B Water bridges: B:K.250, B:K.250 Salt bridges: B:R.200, B:K.209, B:K.250 PO4.10: 5 residues within 4Å: Chain B: K.43, N.248, K.249, K.250, W.251 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.250, B:W.251 Water bridges: B:W.251, B:R.254 Salt bridges: B:K.43 PO4.15: 4 residues within 4Å: Chain C: R.200, K.206, K.209, K.250 7 PLIP interactions: 7 interactions with chain C Water bridges: C:T.85, C:K.250, C:K.250 Salt bridges: C:R.200, C:K.206, C:K.209, C:K.250 PO4.16: 6 residues within 4Å: Chain C: K.43, N.248, K.249, K.250, W.251 Ligands: PO4.17 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.248, C:K.250, C:W.251 Salt bridges: C:K.43 PO4.17: 5 residues within 4Å: Chain C: K.43, K.47, W.251, R.254 Ligands: PO4.16 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:W.251 Salt bridges: C:K.43, C:K.47, C:R.254 PO4.23: 4 residues within 4Å: Chain D: R.200, K.206, K.209, K.250 6 PLIP interactions: 6 interactions with chain D Water bridges: D:K.250, D:K.250 Salt bridges: D:R.200, D:K.206, D:K.209, D:K.250

4 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.6: 4 residues within 4Å: Chain B: Y.210, R.212 Chain D: F.277, E.282 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.212 PG4.8: 8 residues within 4Å: Chain B: A.17, T.180, I.181, V.182, I.239, P.241, D.263, A.264 No protein-ligand interaction detected (PLIP) PG4.12: 7 residues within 4Å: Chain C: A.17, T.180, I.181, E.238, I.239, L.260, A.264 No protein-ligand interaction detected (PLIP) PG4.18: 5 residues within 4Å: Chain B: F.277, E.282 Chain D: Y.210, S.211, R.212 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D Water bridges: B:D.278 Hydrogen bonds: D:R.212

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

CL.11: 2 residues within 4Å: Chain B: H.207 Chain D: A.275 Ligand excluded by PLIP

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.13: 8 residues within 4Å: Chain C: A.82, M.83, D.84, R.140, E.144, L.147, E.217, Y.228 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:D.84, C:D.84, C:R.140, C:Y.228 EDO.21: 7 residues within 4Å: Chain D: A.82, D.84, R.140, E.144, L.147, E.217, Y.228 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:D.84, D:R.140, D:E.217, D:Y.228, D:Y.228 Water bridges: D:A.82, D:D.84

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nocek, B. et al., Crystal structure of Polyphosphate Kinase 2 from Arthrobacter aurescens TC1. TO BE PUBLISHED

Release Date

2011-06-01

Peptides

Putative polyphosphate kinase 2 family protein: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Putative polyphosphate kinase 2 family protein

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