SMTL ID : 3iix.1

X-ray structure of the FeFe-hydrogenase maturase HydE from T. maritima in complex with methionine and 5'deoxyadenosine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.25 Å

Oligo State

monomer

Ligands

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

SF4.1: 9 residues within 4Å: Chain A: C.63, K.65, C.67, Y.69, C.70, R.73, G.109, E.110 Ligands: MET.2 4 PLIP interactions: 4 interactions with chain A, Salt bridges: A:E.110 Metal complexes: A:C.63, A:C.67, A:C.70

1 x MET: METHIONINE(Non-covalent)

MET.2: 10 residues within 4Å: Chain A: Q.107, S.108, S.136, G.138, L.158, R.180, Y.303, L.305 Ligands: SF4.1, 5AD.3 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Q.107 Water bridges: A:G.138, A:E.139, A:E.139, A:E.161, A:R.180 Salt bridges: A:R.180

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

5AD.3: 11 residues within 4Å: Chain A: Y.69, Q.107, R.159, E.161, M.199, P.229, F.230, I.231, L.305, Y.306 Ligands: MET.2 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.305 Hydrogen bonds: A:R.159, A:E.161, A:I.231, A:I.231 Water bridges: A:R.180

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

CPS.4: 6 residues within 4Å: Chain A: V.97, Q.98, F.99, G.100, M.324 Ligands: CPS.8 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Q.98, A:F.99, A:F.99 Hydrogen bonds: A:Q.98 Water bridges: A:K.102 CPS.5: 7 residues within 4Å: Chain A: E.33, F.36, K.37, D.40, R.284 Ligands: CPS.6, CPS.7 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.36, A:R.284 Hydrogen bonds: A:D.40 Water bridges: A:E.33, A:R.284 CPS.6: 10 residues within 4Å: Chain A: R.29, E.33, F.246, T.247, L.250, V.275, I.281 Ligands: CPS.5, CPS.7, CO3.13 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.246, A:L.250, A:V.275, A:I.281 Hydrogen bonds: A:E.33, A:E.33, A:T.247 CPS.7: 3 residues within 4Å: Chain A: R.29 Ligands: CPS.5, CPS.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.29, A:R.29 CPS.8: 4 residues within 4Å: Chain A: M.324, K.325, E.328 Ligands: CPS.4 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:M.324, A:K.325, A:E.328

1 x S3H: trisulfane(Non-covalent)

S3H.9: 6 residues within 4Å: Chain A: R.279, C.311, E.314, C.319, C.322, V.323 No protein-ligand interaction detected (PLIP)

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

CL.10: 5 residues within 4Å: Chain A: R.159, T.268, T.269, A.270, Y.306 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain A: R.54, T.134, R.155 Ligand excluded by PLIP CL.12: 4 residues within 4Å: Chain A: R.159, G.226, P.266, M.291 Ligand excluded by PLIP

1 x CO3: CARBONATE ION(Non-functional Binders)

CO3.13: 3 residues within 4Å: Chain A: D.245, F.246 Ligands: CPS.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.245 Water bridges: A:F.246, A:I.274

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nicolet, Y. et al., Unexpected electron transfer mechanism upon AdoMet cleavage in radical SAM proteins. Proc.Natl.Acad.Sci.USA (2009)

Release Date

2009-09-22

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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