SMTL ID : 5few.1

HydE from T. maritima in complex with S-adenosyl-L-cysteine (final product)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.17 Å

Oligo State

monomer

Ligands

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

SF4.1: 9 residues within 4Å: Chain A: C.73, K.75, C.77, Y.79, C.80, R.83, G.119 Ligands: MET.9, SAH.11 4 PLIP interactions: 4 interactions with chain A, Salt bridges: A:E.120 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 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Q.108, A:F.109 Hydrogen bonds: A:Q.108 Water bridges: A:K.112 CPS.3: 6 residues within 4Å: Chain A: E.43, F.46, K.47, D.50, R.294 Ligands: CPS.5 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.46, A:R.294 Hydrogen bonds: A:D.50 Water bridges: A:E.43 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

2 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 CL.8: 6 residues within 4Å: Chain A: R.169, G.236, P.276, T.278 Ligands: 5X8.10, 41K.12 Ligand excluded by PLIP

1 x MET: METHIONINE(Non-covalent)

MET.9: 11 residues within 4Å: Chain A: Q.117, S.118, S.146, G.148, L.168, R.190, Y.313, L.315 Ligands: SF4.1, 5X8.10, SAH.11 10 PLIP interactions: 8 interactions with chain A, 2 Ligand-Ligand interactions Hydrophobic interactions: A:Q.117 Hydrogen bonds: A:S.118, M.9, M.9 Water bridges: A:G.148, A:E.149, A:E.149, A:E.171, A:R.190 Salt bridges: A:R.190

1 x 5X8: S-adenosyl-L-cysteine(Non-covalent)

5X8.10: 18 residues within 4Å: Chain A: Y.79, C.80, Q.117, R.169, E.171, M.209, P.239, F.240, I.241, T.278, T.279, A.280, L.315, Y.316 Ligands: CL.8, MET.9, SAH.11, 41K.12 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:R.169, A:R.169, A:E.171, A:I.241, A:I.241, A:A.280 Water bridges: A:R.190, A:I.237, A:T.278, A:T.279, A:T.279

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

SAH.11: 21 residues within 4Å: Chain A: Y.79, C.80, Q.117, S.118, 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: SF4.1, MET.9, 5X8.10, 41K.12 16 PLIP interactions: 14 interactions with chain A, 2 Ligand-Ligand interactions Hydrophobic interactions: A:Q.117 Hydrogen bonds: A:S.118, A:R.169, A:E.171, A:E.171, A:I.241, A:I.241, M.9, M.9 Water bridges: A:G.148, A:E.149, A:E.149, A:E.171, 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.12: 12 residues within 4Å: Chain A: I.66, Q.117, L.167, R.169, T.278, T.279, A.280, M.301, Y.316 Ligands: CL.8, 5X8.10, SAH.11 6 PLIP interactions: 6 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 Salt bridges: A:R.169

Links

RCSB   PDBe   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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