SMTL ID : 3k52.2 (1 other biounit)

Crystal Structure of Isopentenyl Phosphate Kinase from M. jannaschii in complex with IP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-tetramer

Ligands

4 x IP8: Isopentenyl phosphate(Non-covalent)

IP8.1: 11 residues within 4Å: Chain A: G.60, G.61, G.65, H.66, I.92, M.96, G.150, D.151, I.162, S.164, G.165 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.92, A:I.162, A:I.162 Hydrogen bonds: A:G.61, A:G.165 Salt bridges: A:K.12, A:H.66 IP8.4: 11 residues within 4Å: Chain B: H.59, G.60, G.61, G.65, H.66, G.150, D.151, I.162, I.163, S.164, G.165 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:I.162, B:I.162 Hydrogen bonds: B:G.61, B:S.164, B:G.165 Water bridges: B:K.12 Salt bridges: B:H.66 IP8.7: 11 residues within 4Å: Chain C: G.60, G.61, G.65, H.66, I.92, M.96, G.150, D.151, I.162, S.164, G.165 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:I.92, C:I.162, C:I.162 Hydrogen bonds: C:G.61, C:G.165 Salt bridges: C:K.12, C:H.66 IP8.10: 11 residues within 4Å: Chain D: H.59, G.60, G.61, G.65, H.66, G.150, D.151, I.162, I.163, S.164, G.165 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:I.162, D:I.162 Hydrogen bonds: D:G.61, D:S.164, D:G.165 Water bridges: D:K.12 Salt bridges: D:H.66

8 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 5 residues within 4Å: Chain A: R.94 Chain C: I.27, K.28, W.29, D.30 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:W.29, C:D.30 Water bridges: C:N.31, A:R.94, A:R.98 Salt bridges: A:R.94 SO4.3: 5 residues within 4Å: Chain A: K.12, G.14, G.15, T.185, K.227 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.15 Salt bridges: A:K.12, A:K.227 SO4.5: 5 residues within 4Å: Chain B: K.12, G.14, G.15, T.185, K.227 4 PLIP interactions: 4 interactions with chain B Water bridges: B:K.12, B:K.12 Salt bridges: B:K.12, B:K.227 SO4.6: 6 residues within 4Å: Chain B: I.27, K.28, W.29, D.30, N.31 Chain C: N.247 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:W.29, B:D.30, B:N.31 SO4.8: 5 residues within 4Å: Chain A: I.27, K.28, W.29, D.30 Chain C: R.94 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:W.29, A:D.30 Water bridges: A:N.31, C:R.94, C:R.98 Salt bridges: C:R.94 SO4.9: 5 residues within 4Å: Chain C: K.12, G.14, G.15, T.185, K.227 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:G.15 Salt bridges: C:K.12, C:K.227 SO4.11: 5 residues within 4Å: Chain D: K.12, G.14, G.15, T.185, K.227 4 PLIP interactions: 4 interactions with chain D Water bridges: D:K.12, D:K.12 Salt bridges: D:K.12, D:K.227 SO4.12: 6 residues within 4Å: Chain A: N.247 Chain D: I.27, K.28, W.29, D.30, N.31 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:W.29, D:D.30, D:N.31

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dellas, N. et al., Mutation of archaeal isopentenyl phosphate kinase highlights mechanism and guides phosphorylation of additional isoprenoid monophosphates. Acs Chem.Biol. (2010)

Release Date

2010-05-05

Peptides

isopentenyl phosphate kinase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

isopentenyl phosphate kinase

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