SMTL ID : 4ck0.1

Crystal structure of the integral membrane diacylglycerol kinase - form 2

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.92 Å

Oligo State

homo-trimer

Ligands

2 x OLC: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate(Non-covalent)

OLC.1: 15 residues within 4Å: Chain A: R.18, A.22, A.23, S.26 Chain B: A.39, E.43, A.46, I.53, E.78, N.81, S.107, V.110, L.111, I.114 Ligands: OLC.2 8 PLIP interactions: 2 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:R.18, A:S.26, B:E.43, B:N.81 Hydrophobic interactions: B:A.46, B:I.53, B:L.111, B:I.114 OLC.2: 10 residues within 4Å: Chain A: I.19 Chain B: Q.42, E.43, A.46, V.71, I.114, W.121, C.122, L.125 Ligands: OLC.1 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:E.43, B:V.71, B:I.114, B:W.121, B:W.121, B:L.125 Hydrogen bonds: B:Q.42

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 3 residues within 4Å: Chain C: E.37, E.85 Ligands: ACP.5 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.37, C:E.85 ZN.4: 2 residues within 4Å: Chain C: E.85 Ligands: ACP.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:E.85

1 x ACP: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER(Non-covalent)

ACP.5: 14 residues within 4Å: Chain B: R.18, K.21, Y.25 Chain C: E.37, E.85, E.94, Y.95, H.96, S.99, G.100, K.103, D.104 Ligands: ZN.3, ZN.4 8 PLIP interactions: 6 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:E.37, C:E.85, C:E.94, C:H.96, C:D.104, B:R.18, B:K.21 Salt bridges: C:K.103

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, D. et al., Crystal Structure of the Integral Membrane Diacylglycerol Kinase with Zn-Amppcp Bound and its Catalytic Mechanism. To be Published

Release Date

2015-01-28

Peptides

DIACYLGLYCEROL KINASE: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Membrane

We predict this structure to be a membrane protein.
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DIACYLGLYCEROL KINASE

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