SMTL ID : 5fez.1

HydE from T. maritima in complex with (2R,4R)-MeSeTDA, 5'-deoxyadenosine and methionine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

monomer

Ligands

1 x SFS: Fe4-Se4 cluster(Non-covalent)

SFS.1: 8 residues within 4Å: Chain A: C.73, K.75, C.77, Y.79, C.80, R.83, G.119 Ligands: MET.9 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.73, A:C.77, A:C.80

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

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

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

CL.7: 4 residues within 4Å: Chain A: R.64, T.113, T.144, R.165 Ligand excluded by PLIP

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

5AD.8: 13 residues within 4Å: Chain A: Y.79, C.80, Q.117, R.169, E.171, M.209, P.239, F.240, I.241, L.315, Y.316 Ligands: MET.9, 9SE.10 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.315 Hydrogen bonds: A:R.169, A:E.171, A:I.241, A:I.241 Water bridges: A:R.190, A:H.243

1 x MET: METHIONINE(Non-covalent)

MET.9: 10 residues within 4Å: Chain A: Q.117, S.118, S.146, G.148, L.168, R.190, Y.313, L.315 Ligands: SFS.1, 5AD.8 7 PLIP interactions: 6 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:Q.117 Water bridges: A:G.148, A:E.149, A:E.171, A:R.190, M.9 Salt bridges: A:R.190

1 x 9SE: (2~{R},4~{R})-2-methyl-1,3-selenazolidine-2,4-dicarboxylic acid(Non-covalent)

9SE.10: 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: 5AD.8 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rohac, R. et al., Carbon-sulfur bond-forming reaction catalysed by the radical SAM enzyme HydE. Nat.Chem. (2016)

Release Date

2016-04-06

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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