SMTL ID : 4uxw.1

Structure of delta4-DgkA-apo in 9.9 MAG

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.15 Å

Oligo State

homo-trimer

Ligands

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

OLC.1: 12 residues within 4Å: Chain A: W.27, L.30, R.31, W.34, I.35, V.47, V.51, C.55, M.72 Chain B: I.112, I.115, I.119 8 PLIP interactions: 2 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:I.112, B:I.115, A:W.27, A:L.30, A:L.30, A:V.47, A:V.51 Hydrogen bonds: A:R.31 OLC.2: 11 residues within 4Å: Chain A: A.39, Q.42, E.43, A.46, I.53, V.71, V.74, I.114, A.117, W.121, L.125 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:A.117, A:W.121, A:W.121, A:W.121, A:L.125 Hydrogen bonds: A:Q.42 OLC.4: 16 residues within 4Å: Chain A: A.22, A.23, S.26 Chain B: A.39, E.43, A.46, L.49, A.50, I.53, E.78, S.107, V.110, L.111, I.114, W.121 Ligands: OLC.5 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:A.46, B:L.49, B:A.50, B:I.53, B:L.111, B:I.114, B:I.114, B:W.121 Hydrogen bonds: B:E.78, B:N.81, A:S.26 OLC.5: 12 residues within 4Å: Chain A: I.19 Chain B: Q.42, E.43, A.46, V.47, V.71, I.114, V.118, W.121, C.122, W.126 Ligands: OLC.4 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:E.43, B:V.47, B:V.71, B:I.114, B:V.118, B:W.121, B:W.121, B:W.126 Hydrogen bonds: B:Q.42 OLC.8: 15 residues within 4Å: Chain B: G.15, R.18, I.19 Chain C: A.39, Q.42, E.43, A.46, V.71, V.74, E.78, I.114, A.117, V.118, W.121 Ligands: OLC.9 12 PLIP interactions: 11 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:Q.42, C:A.46, C:V.71, C:V.74, C:I.114, C:A.117, C:V.118, C:W.121, C:W.121, B:I.19 Hydrogen bonds: C:Q.42, C:Q.42 OLC.9: 13 residues within 4Å: Chain B: A.22, A.23, S.26 Chain C: E.78, N.81, S.107, V.110, L.111, I.115, V.118 Ligands: NO3.6, NA.7, OLC.8 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:I.115, B:A.23 Hydrogen bonds: C:E.78, C:N.81, B:S.26

1 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.3: 4 residues within 4Å: Chain B: Y.25 Chain C: K.103, D.104 Ligands: NO3.6 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Y.25, B:Y.25 Hydrogen bonds: B:Y.25, B:Y.25

1 x NO3: NITRATE ION(Non-functional Binders)

NO3.6: 7 residues within 4Å: Chain B: A.22, Y.25 Chain C: E.85, S.107 Ligands: MPD.3, NA.7, OLC.9 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.107, C:S.107

1 x NA: SODIUM ION(Non-functional Binders)

NA.7: 5 residues within 4Å: Chain C: E.37, N.81, E.85 Ligands: NO3.6, OLC.9 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.37, C:N.81

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, D. et al., Ternary Structure Reveals Mechanism of a Membrane Diacylglycerol Kinase. Nat.Commun. (2015)

Release Date

2015-09-30

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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