SMTL ID : 3lkk.1

Crystal structure of the isopentenyl phosphate kinase substrate complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 22 residues within 4Å: Chain A: K.9, G.11, G.12, S.13, K.18, G.48, G.49, G.50, H.54, T.167, D.168, V.169, G.171, I.172, Y.173, K.175, D.176, P.177, K.178, I.206, K.209 Ligands: IP8.2 26 PLIP interactions: 26 interactions with chain A Hydrogen bonds: A:G.12, A:S.13, A:S.13, A:G.49, A:G.50, A:D.168, A:Y.173, A:Y.173, A:K.178, A:I.206 Water bridges: A:K.9, A:K.9, A:K.9, A:K.18, A:K.18, A:G.147, A:K.209 Salt bridges: A:K.9, A:K.9, A:K.18, A:K.18, A:K.18, A:H.54, A:K.209, A:K.209, A:K.209 ATP.3: 21 residues within 4Å: Chain B: K.9, G.11, G.12, S.13, K.18, G.48, G.49, G.50, H.54, D.168, V.169, G.171, I.172, Y.173, K.175, D.176, P.177, K.178, I.206, K.209 Ligands: IP8.4 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:G.12, B:S.13, B:G.49, B:G.50, B:D.168, B:Y.173, B:Y.173, B:K.178, B:K.178 Water bridges: B:K.18, B:K.18, B:K.18 Salt bridges: B:K.9, B:K.9, B:K.18, B:K.18, B:K.18, B:H.54, B:K.209, B:K.209

2 x IP8: Isopentenyl phosphate(Non-covalent)

IP8.2: 14 residues within 4Å: Chain A: K.9, G.48, G.49, G.50, G.53, H.54, V.77, M.81, G.132, D.133, I.144, S.146, G.147 Ligands: ATP.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:V.77, A:I.144 Hydrogen bonds: A:G.49, A:G.50, A:G.147 Water bridges: A:K.9, A:K.9, A:D.148 Salt bridges: A:K.9, A:H.54 IP8.4: 14 residues within 4Å: Chain B: K.9, G.48, G.49, G.50, G.53, H.54, V.77, M.81, G.132, D.133, I.144, S.146, G.147 Ligands: ATP.3 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:V.77, B:I.144, B:I.144 Hydrogen bonds: B:G.49, B:G.50, B:G.147 Salt bridges: B:K.9, B:H.54

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mabanglo, M.F. et al., X-ray structures of isopentenyl phosphate kinase. Acs Chem.Biol. (2010)

Release Date

2010-06-02

Peptides

Gamma-glutamyl kinase related protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Gamma-glutamyl kinase related protein

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