SMTL ID : 7tol.1

X-ray crystal structure of glycerol dibiphytanyl glycerol tetraether - macrocyclic archaeol synthase (GDGT-MAS) from Methanocaldococcus jannaschii with archaeal lipid, 5'deoxyadenosine, and methionine bound

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.03 Å

Oligo State

monomer

Ligands

1 x FE: FE (III) ION(Non-covalent)

FE.1: 4 residues within 4Å: Chain A: C.29, C.32, C.53, H.56 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.29, A:C.32, A:C.53, A:H.56

3 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.2: 11 residues within 4Å: Chain A: C.118, L.120, C.122, I.124, C.125, G.165, N.193, Q.217, R.230, R.295 Ligands: MET.6 4 PLIP interactions: 1 Ligand-Ligand interactions, 3 interactions with chain A Metal complexes: MET.6, A:C.118, A:C.122, A:C.125 SF4.3: 11 residues within 4Å: Chain A: C.93, P.94, D.96, C.97, L.99, C.100, N.102, H.103, V.472, M.473, P.488 5 PLIP interactions: 5 interactions with chain A, Salt bridges: A:D.96 Metal complexes: A:C.93, A:C.97, A:C.100, A:H.103 SF4.4: 13 residues within 4Å: Chain A: S.354, C.358, M.459, H.460, F.461, M.462, R.471, V.472, C.475, C.476, I.477, F.489, C.490 3 PLIP interactions: 3 interactions with chain A, Metal complexes: A:C.358, A:C.475, A:C.490

1 x 5AD: 5'-DEOXYADENOSINE(Non-covalent)

5AD.5: 13 residues within 4Å: Chain A: I.124, C.125, F.126, Q.217, R.230, V.256, T.258, Q.288, P.289, V.290, S.291 Ligands: MET.6, L4P.9 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.126 Hydrogen bonds: A:F.126, A:Q.217, A:R.230, A:R.230, A:T.258, A:T.258, A:Q.288, A:S.291, A:S.291 Water bridges: A:C.125, A:Q.217 pi-Stacking: A:F.126

1 x MET: METHIONINE(Non-covalent)

MET.6: 11 residues within 4Å: Chain A: F.126, A.127, G.164, G.165, E.166, A.191, T.192, N.193, Q.217 Ligands: SF4.2, 5AD.5 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.191 Hydrogen bonds: A:G.165, A:Q.217

1 x L1P: 3-PHOSPHORYL-[1,2-DI-PHYTANYL]GLYCEROL(Non-covalent)

L1P.7: 24 residues within 4Å: Chain A: I.108, P.158, A.159, L.186, H.187, N.286, V.331, V.334, S.338, V.341, D.347, K.349, P.350, L.352, T.360, Y.363, I.435, S.441, Y.443, L.446, H.450, S.457, C.458 Ligands: L4P.9 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:I.108, A:P.158, A:A.159, A:V.334, A:V.341, A:L.352, A:Y.363, A:I.435, A:Y.443, A:L.446 Water bridges: A:R.151, A:R.348 Salt bridges: A:K.349

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.8: 6 residues within 4Å: Chain A: T.168, V.169, K.196, N.199, Y.202, G.518 No protein-ligand interaction detected (PLIP)

1 x L4P: 3-[GLYCEROLYLPHOSPHONYL]-[1,2-DI-PHYTANYL]GLYCEROL(Non-covalent)

L4P.9: 35 residues within 4Å: Chain A: L.109, N.111, F.126, Q.161, H.187, Q.189, K.207, L.211, S.212, T.213, Y.215, F.250, S.252, V.254, R.283, N.286, Q.288, Y.329, P.330, V.331, S.333, V.334, S.361, Y.363, Y.443, L.446, A.447, H.450, Y.451, M.455, F.461, I.477, F.489 Ligands: 5AD.5, L1P.7 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:Y.215, A:V.254, A:Y.329, A:V.334, A:Y.363, A:Y.363, A:Y.443, A:L.446, A:F.461, A:I.477, A:F.489 Hydrogen bonds: A:K.207, A:S.212 Water bridges: A:R.181, A:R.181, A:R.181, A:R.181, A:S.212, A:S.212

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lloyd, C.T. et al., Discovery, structure and mechanism of a tetraether lipid synthase. Nature (2022)

Release Date

2022-08-31

Peptides

glycerol dibiphytanyl glycerol tetraether - macrocyclic archaeol synthase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

glycerol dibiphytanyl glycerol tetraether - macrocyclic archaeol synthase

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