SMTL ID : 3iiz.1

X-ray structure of the FeFe-hydrogenase maturase HydE from T. maritima in complex with S-adenosyl-L-methionine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.62 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: SAM.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Salt bridges: A:E.110 Metal complexes: A:C.63, A:C.67, A:C.70, SAM.2

1 x SAM: S-ADENOSYLMETHIONINE(Non-covalent)

SAM.2: 17 residues within 4Å: Chain A: Y.69, C.70, Q.107, S.108, S.136, G.138, R.159, E.161, R.180, M.199, P.229, F.230, I.231, Y.303, L.305, Y.306 Ligands: SF4.1 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Q.107 Hydrogen bonds: A:E.110, A:R.159, A:E.161, A:I.231, A:I.231 Water bridges: A:S.136, A:G.138, A:E.139, A:E.161, A:R.180, A:R.180, A:R.180 Salt bridges: A:R.180

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

CPS.3: 8 residues within 4Å: Chain A: V.97, Q.98, F.99, G.100, K.102, P.321, M.324 Ligands: CPS.7 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Q.98, A:F.99, A:P.321 Hydrogen bonds: A:Q.98 Water bridges: A:K.102, A:K.102 Salt bridges: A:K.102 CPS.4: 7 residues within 4Å: Chain A: F.36, K.37, D.40, R.284, C.285 Ligands: CPS.5, CPS.6 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:K.37 CPS.5: 10 residues within 4Å: Chain A: R.29, E.33, F.246, T.247, L.250, V.275, I.281 Ligands: CPS.4, CPS.6, 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.6: 3 residues within 4Å: Chain A: R.29 Ligands: CPS.4, CPS.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.29, A:R.29 CPS.7: 4 residues within 4Å: Chain A: M.324, K.325, E.328 Ligands: CPS.3 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:M.324, A:K.325, A:E.328

1 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)

FES.8: 8 residues within 4Å: Chain A: R.279, P.292, C.311, C.319, C.322, V.323 Ligands: H2S.9, H2S.10 1 PLIP interactions: 1 interactions with chain A, Metal complexes: A:C.311

2 x H2S: HYDROSULFURIC ACID(Non-covalent)

H2S.9: 4 residues within 4Å: Chain A: C.311, E.314, C.319 Ligands: FES.8 No protein-ligand interaction detected (PLIP) H2S.10: 5 residues within 4Å: Chain A: R.279, C.322, V.323, M.326 Ligands: FES.8 No protein-ligand interaction detected (PLIP)

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

CL.11: 4 residues within 4Å: Chain A: R.54, T.103, T.134, R.155 Ligand excluded by PLIP CL.12: 5 residues within 4Å: Chain A: R.159, T.268, T.269, A.270, Y.306 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.5 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.243

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

Biotin synthetase, putative: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Biotin synthetase, putative

Related Entries With Identical Sequence