SMTL ID : 3a9y.1

Crystal structure of rat selenocysteine lyase in complex with L-cysteine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

2 x CYS: CYSTEINE(Non-covalent)

CYS.1: 12 residues within 4Å: Chain A: N.25, A.26, H.133, N.186, Q.224, K.247, A.373, S.374, C.375, R.402 Chain B: N.48 Ligands: PLP.3 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.186, A:S.374, A:S.374, B:N.48 Salt bridges: A:R.402 CYS.5: 13 residues within 4Å: Chain A: N.48 Chain B: N.25, A.26, H.133, N.186, Q.224, K.247, G.372, A.373, S.374, C.375, R.402 Ligands: PLP.6 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:N.48, B:N.186, B:S.374, B:S.374 Salt bridges: B:R.402

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: L.332, N.333, S.334, R.335, F.336 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.332, A:N.333, A:R.335 Water bridges: A:V.159

2 x PLP: PYRIDOXAL-5'-PHOSPHATE(Covalent)

PLP.3: 16 residues within 4Å: Chain A: G.87, T.88, N.91, H.133, S.135, M.182, N.186, D.221, A.223, Q.224, V.244, H.246, K.247 Chain B: G.283, T.284 Ligands: CYS.1 18 PLIP interactions: 3 interactions with chain B, 14 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: B:T.284, B:T.284, A:G.87, A:T.88, A:T.88, A:N.91, A:Q.224 Water bridges: B:Q.276, A:T.88, A:H.246, C.1 Hydrophobic interactions: A:H.133, A:A.223, A:K.247 Salt bridges: A:H.133, A:H.246, A:K.247 pi-Stacking: A:H.133 PLP.6: 16 residues within 4Å: Chain A: G.283, T.284 Chain B: G.87, T.88, N.91, H.133, S.135, M.182, N.186, D.221, A.223, Q.224, V.244, H.246, K.247 Ligands: CYS.5 17 PLIP interactions: 12 interactions with chain B, 4 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: B:H.133, B:A.223, B:K.247 Hydrogen bonds: B:G.87, B:T.88, B:Q.224, A:Q.276, A:T.284, A:T.284, A:T.284 Water bridges: B:T.88, B:H.246, C.5 Salt bridges: B:H.133, B:H.246, B:K.247 pi-Stacking: B:H.133

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.4: 3 residues within 4Å: Chain A: R.312, R.315, R.341 6 PLIP interactions: 6 interactions with chain A Water bridges: A:R.312, A:R.315, A:R.341, A:R.341 Salt bridges: A:R.315, A:R.341

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Omi, R. et al., Reaction mechanism and molecular basis for selenium/sulfur discrimination of selenocysteine lyase. J.Biol.Chem. (2010)

Release Date

2010-03-16

Peptides

Selenocysteine lyase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Selenocysteine lyase

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