SMTL ID : 8qml.1

(2R,4R)-MeTDA bound HydE structure (control experiment)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

monomer

Ligands

1 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.1: 20 residues within 4Å: Chain A: Y.79, C.80, Q.117, S.118, G.119, S.146, G.148, L.168, R.169, E.171, R.190, M.209, P.239, F.240, I.241, Y.313, L.315, Y.316 Ligands: 41K.2, SF4.8 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:Q.117 Hydrogen bonds: A:R.169, A:E.171, A:I.241, A:I.241 Water bridges: A:S.146, A:G.148, A:E.149, A:E.171, A:R.190, A:R.190, A:R.190 Salt bridges: A:R.190

1 x 41K: (2R,4R)-2-methyl-1,3-thiazolidine-2,4-dicarboxylic acid(Non-covalent)

41K.2: 12 residues within 4Å: Chain A: I.66, Q.117, L.167, R.169, G.236, P.276, T.278, T.279, A.280, M.301, Y.316 Ligands: SAH.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.66 Hydrogen bonds: A:R.169, A:T.279, A:A.280 Water bridges: A:T.279, A:Y.316 Salt bridges: A:R.169

5 x CPS: 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE(Non-covalent)

CPS.3: 6 residues within 4Å: Chain A: V.107, Q.108, F.109, G.110, P.331, M.334 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Q.108, A:F.109, A:P.331 Hydrogen bonds: A:Q.108 Water bridges: A:K.112 CPS.4: 7 residues within 4Å: Chain A: E.43, F.46, K.47, D.50, R.294 Ligands: CPS.5, CPS.6 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:E.43, A:F.46, A:R.294 Hydrogen bonds: A:D.50 Water bridges: A:R.294 CPS.5: 9 residues within 4Å: Chain A: R.39, E.43, F.256, T.257, L.260, V.285, I.291 Ligands: CPS.4, CPS.6 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.256, A:L.260, A:V.285, A:V.285 Hydrogen bonds: A:R.39, A:E.43, A:E.43, A:T.257 CPS.6: 3 residues within 4Å: Chain A: R.39 Ligands: CPS.4, CPS.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.39 CPS.7: 2 residues within 4Å: Chain A: P.331, E.338 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.331, A:E.338

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

SF4.8: 8 residues within 4Å: Chain A: C.73, K.75, C.77, Y.79, C.80, R.83, G.119 Ligands: SAH.1 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Salt bridges: A:E.120 Metal complexes: A:C.73, A:C.77, A:C.80, SAH.1

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.9: 4 residues within 4Å: Chain A: R.64, T.113, T.144, R.165 Ligand excluded by PLIP

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.10: 5 residues within 4Å: Chain A: K.112, G.140, R.346, D.347, W.348 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.346

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Omeiri, J. et al., Maturation of the [FeFe]-Hydrogenase: Direct Transfer of the ( kappa 3 -cysteinate)Fe II (CN)(CO) 2 Complex B from HydG to HydE. Angew.Chem.Int.Ed.Engl. (2023)

Release Date

2023-11-22

Peptides

[FeFe] hydrogenase maturase subunit HydE: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

[FeFe] hydrogenase maturase subunit HydE

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