SMTL ID : 3oz2.1

Crystal structure of a geranylgeranyl bacteriochlorophyll reductase-like (Ta0516) from Thermoplasma acidophilum at 1.60 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

1 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.1: 35 residues within 4Å: Chain A: V.10, G.11, G.12, G.13, P.14, G.15, E.34, K.35, R.36, R.44, C.45, G.46, E.47, G.48, R.101, P.124, A.125, A.157, D.158, G.159, E.163, A.183, F.214, G.263, G.264, V.265, G.283, D.284, I.289, G.294, G.295, G.296, I.297, A.300 Ligands: OZ2.2 29 PLIP interactions: 29 interactions with chain A Hydrophobic interactions: A:A.183, A:V.265 Hydrogen bonds: A:G.12, A:G.13, A:G.15, A:K.35, A:G.46, A:G.48, A:G.48, A:R.101, A:R.101, A:A.125, A:E.163, A:E.163, A:D.284, A:G.296, A:I.297 Water bridges: A:G.12, A:G.16, A:K.35, A:R.36, A:R.36, A:R.36, A:G.40, A:G.159, A:F.160, A:D.284, A:A.285, A:A.298

1 x OZ2: (2R)-3-{[(R)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-2-[(6Z)-tridec-6-enoyloxy]propyl (9Z)-octadec-9-enoate(Non-covalent)

OZ2.2: 22 residues within 4Å: Chain A: I.181, F.200, G.209, Y.210, W.212, F.214, V.265, V.267, P.291, I.292, T.293, G.294, G.295, K.339, K.347, L.350, I.373, S.374, V.375 Ligands: FAD.1, EDO.8, GOL.15 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:I.181, A:F.200, A:F.200, A:Y.210, A:Y.210, A:W.212, A:W.212, A:F.214, A:V.265, A:V.267, A:K.347, A:L.350 Hydrogen bonds: A:V.375 Water bridges: A:R.342, A:R.342 Salt bridges: A:K.339

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

EDO.3: 4 residues within 4Å: Chain A: V.119, W.120, V.121, H.142 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:V.121, A:V.121 Water bridges: A:W.120, A:H.142, A:N.143 EDO.4: 3 residues within 4Å: Chain A: K.312, E.313, E.316 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.316, A:E.316 EDO.5: 6 residues within 4Å: Chain A: K.130, G.133, K.134, V.135, M.276, P.277 No protein-ligand interaction detected (PLIP) EDO.6: 5 residues within 4Å: Chain A: T.4, Y.5, R.150, A.151, K.152 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.5, A:Y.5 EDO.7: 5 residues within 4Å: Chain A: N.178, S.228, W.231, K.347, E.348 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.228, A:K.347 Water bridges: A:N.178, A:E.348 EDO.8: 6 residues within 4Å: Chain A: D.290, T.293, G.295, N.299 Ligands: OZ2.2, EDO.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.293 EDO.9: 6 residues within 4Å: Chain A: A.298, N.299, V.302, R.335, K.339 Ligands: EDO.8 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.335, A:K.339, A:K.339 Water bridges: A:N.299 EDO.10: 3 residues within 4Å: Chain A: Y.5, D.118, W.120 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.118, A:V.119 EDO.11: 6 residues within 4Å: Chain A: N.132, G.133, K.134, P.277, Y.320, S.321 No protein-ligand interaction detected (PLIP) EDO.12: 5 residues within 4Å: Chain A: A.24, G.27, L.28, K.29, A.115 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.115 Water bridges: A:G.27 EDO.13: 4 residues within 4Å: Chain A: S.172, V.270, K.271, M.272 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.270

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.14: 8 residues within 4Å: Chain A: P.273, T.275, M.276, P.277, P.322, M.325, Q.326, E.329 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.275, A:T.275, A:Q.326 GOL.15: 7 residues within 4Å: Chain A: G.48, L.49, S.50, V.70, V.95, T.198 Ligands: OZ2.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.48, A:V.95, A:Y.97, A:Y.97, A:T.198

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, Q. et al., Insights into substrate specificity of geranylgeranyl reductases revealed by the structure of digeranylgeranylglycerophospholipid reductase, an essential enzyme in the biosynthesis of archaeal membrane lipids. J.Mol.Biol. (2010)

Release Date

2010-10-27

Peptides

Digeranylgeranylglycerophospholipid reductase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Digeranylgeranylglycerophospholipid reductase