SMTL ID : 3cix.1

X-RAY structure of the [FeFe]-hydrogenase maturase HydE from thermotoga maritima in complex with thiocyanate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

1 x SCN: THIOCYANATE ION(Non-functional Binders)

SCN.1: 5 residues within 4Å: Chain A: R.54, T.103, T.134, R.155, M.224 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.134, A:R.155

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

CL.2: 4 residues within 4Å: Chain A: T.268, T.269, A.270, Y.306 Ligand excluded by PLIP CL.3: 4 residues within 4Å: Chain A: R.159, G.226, P.266, T.268 Ligand excluded by PLIP

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

SF4.4: 9 residues within 4Å: Chain A: C.63, K.65, C.67, Y.69, C.70, R.73, G.109, E.110 Ligands: SAH.5 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, SAH.5

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

SAH.5: 19 residues within 4Å: Chain A: Y.69, C.70, Q.107, S.108, G.109, 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: SF4.4 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.161, 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.6: 6 residues within 4Å: Chain A: V.97, Q.98, F.99, G.100, M.324 Ligands: CPS.11 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Q.98, A:F.99 Hydrogen bonds: A:Q.98 CPS.8: 6 residues within 4Å: Chain A: F.36, K.37, D.40, R.284 Ligands: CPS.9, CPS.10 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:E.41 CPS.9: 10 residues within 4Å: Chain A: R.29, E.33, F.246, T.247, L.250, V.275, I.281 Ligands: CPS.8, CPS.10, GOL.14 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.246, A:L.250, A:V.275, A:V.275, A:I.281, A:I.281 Hydrogen bonds: A:E.33, A:E.33, A:T.247 CPS.10: 3 residues within 4Å: Chain A: R.29 Ligands: CPS.8, CPS.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.29, A:R.29 CPS.11: 4 residues within 4Å: Chain A: M.324, K.325, E.328 Ligands: CPS.6 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:M.324, A:K.325, A:E.328

1 x SAT: sulfoacetic acid(Non-functional Binders)

SAT.7: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

FES.12: 5 residues within 4Å: Chain A: R.279, C.311, C.319, C.322, V.323 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions, Metal complexes: A:C.311, A:C.319, A:C.322, H2O.1

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.13: 5 residues within 4Å: Chain A: D.337, W.338, G.339, G.340, K.342 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:K.342 Hydrogen bonds: A:W.338, A:G.339, A:G.340, A:K.342

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.14: 7 residues within 4Å: Chain A: K.243, G.244, D.245, F.246, I.274, V.275 Ligands: CPS.9 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.244, A:F.246 Water bridges: A:D.245, A:D.245

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nicolet, Y. et al., X-ray Structure of the [FeFe]-Hydrogenase Maturase HydE from Thermotoga maritima. J.Biol.Chem. (2008)

Release Date

2008-04-08

Peptides

FeFe-Hydrogenase maturase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

FeFe-Hydrogenase maturase

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