SMTL ID : 5ff3.1

HydE from T. maritima in complex with 4R-TCA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.18 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, L.72, R.73, G.109 Ligands: SAH.10 4 PLIP interactions: 4 interactions with chain A, Salt bridges: A:E.110 Metal complexes: A:C.63, A:C.67, A:C.70

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

CPS.2: 6 residues within 4Å: Chain A: V.97, Q.98, F.99, G.100, M.324 Ligands: CPS.6 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Q.98, A:F.99 Hydrogen bonds: A:Q.98 CPS.3: 6 residues within 4Å: Chain A: E.33, F.36, K.37, D.40, R.284 Ligands: CPS.5 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.36, A:R.284 Hydrogen bonds: A:D.40 Water bridges: A:E.33, A:E.41, A:R.284 CPS.4: 8 residues within 4Å: Chain A: R.29, E.33, F.246, T.247, L.250, V.275, I.281 Ligands: CPS.5 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.246, A:L.250, A:V.275 Hydrogen bonds: A:R.29, A:E.33, A:E.33, A:T.247 Water bridges: A:R.29 CPS.5: 3 residues within 4Å: Chain A: R.29 Ligands: CPS.3, CPS.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.29 Water bridges: A:R.29, A:R.29 CPS.6: 3 residues within 4Å: Chain A: P.321, E.328 Ligands: CPS.2 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.321, A:E.328

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

CL.7: 4 residues within 4Å: Chain A: R.54, T.103, T.134, R.155 Ligand excluded by PLIP CL.8: 6 residues within 4Å: Chain A: R.159, G.226, P.266, T.268, M.291 Ligands: PRS.13 Ligand excluded by PLIP

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

FES.9: 7 residues within 4Å: Chain A: R.279, C.311, E.314, C.319, C.322, V.323 Ligands: H2S.12 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.311, A:C.319, A:C.322, H2O.12

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

SAH.10: 19 residues within 4Å: Chain A: Y.69, C.70, Q.107, S.108, S.136, G.138, L.158, R.159, E.161, R.180, M.199, P.229, F.230, I.231, Y.303, L.305, Y.306 Ligands: SF4.1, PRS.13 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Q.107 Hydrogen bonds: A:R.159, A:E.161, A:I.231, A:I.231 Water bridges: A:G.138, A:E.139, A:E.161, A:E.161, A:R.180, A:R.180 Salt bridges: A:R.180

2 x H2S: HYDROSULFURIC ACID(Non-covalent)(Covalent)

H2S.11: 1 residues within 4Å: Chain A: C.322 No protein-ligand interaction detected (PLIP) H2S.12: 3 residues within 4Å: Chain A: C.311, C.319 Ligands: FES.9 No protein-ligand interaction detected (PLIP)

1 x PRS: THIOPROLINE(Non-covalent)

PRS.13: 9 residues within 4Å: Chain A: Q.107, R.159, T.268, T.269, A.270, L.305, Y.306 Ligands: CL.8, SAH.10 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.269, A:A.270 Water bridges: A:R.159, A:R.159, A:T.269, A:Y.306

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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