SMTL ID : 3a9z.1

Crystal structure of ras selenocysteine lyase in complex with selenopropionate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-dimer

Ligands

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

PLP.1: 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: SLP.2 17 PLIP interactions: 14 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:H.133, A:A.223, A:K.247 Hydrogen bonds: A:G.87, A:T.88, A:T.88, A:T.88, A:Q.224, A:K.247, B:T.284 Water bridges: A:H.246, B:Q.276, B:Q.276 Salt bridges: A:H.133, A:H.246, A:K.247 pi-Stacking: A:H.133 PLP.5: 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: SLP.6 17 PLIP interactions: 14 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:H.133, B:A.223, B:K.247 Hydrogen bonds: B:G.87, B:T.88, B:T.88, B:N.91, B:Q.224, B:K.247, A:T.284, A:T.284 Water bridges: B:H.246, A:Q.276 Salt bridges: B:H.133, B:H.246, B:K.247 pi-Stacking: B:H.133

2 x SLP: 3-SELANYLPROPANOIC ACID(Non-covalent)

SLP.2: 9 residues within 4Å: Chain A: N.25, A.26, H.133, N.186, K.247, A.373, S.374, R.402 Ligands: PLP.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.186, A:S.374, A:S.374 Salt bridges: A:R.402 SLP.6: 10 residues within 4Å: Chain B: N.25, A.26, H.133, N.186, Q.224, K.247, A.373, S.374, R.402 Ligands: PLP.5 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.186, B:Q.224, B:S.374, B:S.374 Salt bridges: B:R.402

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

PO4.3: 2 residues within 4Å: Chain A: G.352, S.353 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.353, A:S.353 Water bridges: A:Q.354, A:E.429 PO4.4: 3 residues within 4Å: Chain A: H.310, D.313, R.411 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:A.309, A:R.411 Water bridges: A:H.310, A:R.411, A:R.411 Salt bridges: A:H.310

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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