SMTL ID : 1ibj.1

Crystal structure of cystathionine beta-lyase from Arabidopsis thaliana

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

4 x CO3: CARBONATE ION(Non-functional Binders)

CO3.1: 6 residues within 4Å: Chain A: Y.181, K.278, S.405, F.406, R.440 Ligands: PLP.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.405 Water bridges: A:N.228 CO3.4: 7 residues within 4Å: Chain B: N.228, K.278, V.404, S.405, F.406, R.440 Ligands: PLP.5 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.405, B:R.440, B:R.440 CO3.6: 6 residues within 4Å: Chain C: Y.181, K.278, S.405, F.406, R.440 Ligands: PLP.8 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.405 Water bridges: C:N.228 CO3.9: 7 residues within 4Å: Chain D: N.228, K.278, V.404, S.405, F.406, R.440 Ligands: PLP.10 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.405, D:R.440, D:R.440

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 5 residues within 4Å: Chain A: P.364, G.365, H.366, H.367, L.368 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.365, A:H.367, A:L.368 SO4.7: 5 residues within 4Å: Chain C: P.364, G.365, H.366, H.367, L.368 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:G.365, C:H.367, C:L.368

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

PLP.3: 18 residues within 4Å: Chain A: S.156, G.157, M.158, L.161, Y.181, E.224, D.253, S.255, M.273, S.275, T.277, K.278, M.287, A.288, F.406 Chain B: Y.127, R.129 Ligands: CO3.1 16 PLIP interactions: 14 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:Y.181, A:Y.181, A:K.278 Hydrogen bonds: A:S.156, A:G.157, A:M.158, A:S.255, A:S.275, A:T.277, B:Y.127 Water bridges: A:S.184, A:E.224, A:N.228 Salt bridges: A:K.278, B:R.129 pi-Stacking: A:Y.181 PLP.5: 18 residues within 4Å: Chain A: Y.127, R.129 Chain B: S.156, G.157, M.158, L.161, Y.181, E.224, D.253, S.255, M.273, S.275, T.277, K.278, M.287, A.288, F.406 Ligands: CO3.4 12 PLIP interactions: 9 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:Y.181, B:K.278 Hydrogen bonds: B:S.156, B:G.157, B:M.158, B:S.255, A:Y.127, A:Y.127 Water bridges: B:S.184 Salt bridges: B:K.278, A:R.129 pi-Stacking: B:Y.181 PLP.8: 18 residues within 4Å: Chain C: S.156, G.157, M.158, L.161, Y.181, E.224, D.253, S.255, M.273, S.275, T.277, K.278, M.287, A.288, F.406 Chain D: Y.127, R.129 Ligands: CO3.6 16 PLIP interactions: 13 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:Y.181, C:Y.181, C:K.278 Hydrogen bonds: C:S.156, C:G.157, C:M.158, C:S.255, C:S.275, D:Y.127, D:Y.127 Water bridges: C:E.224, C:N.228, C:D.253 Salt bridges: C:K.278, D:R.129 pi-Stacking: C:Y.181 PLP.10: 18 residues within 4Å: Chain C: Y.127, R.129 Chain D: S.156, G.157, M.158, L.161, Y.181, E.224, D.253, S.255, M.273, S.275, T.277, K.278, M.287, A.288, F.406 Ligands: CO3.9 12 PLIP interactions: 10 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:Y.181, D:K.278 Hydrogen bonds: D:S.156, D:G.157, D:M.158, D:S.255, D:T.277, C:Y.127 Water bridges: D:E.224 Salt bridges: D:K.278, C:R.129 pi-Stacking: D:Y.181

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Breitinger, U. et al., The three-dimensional structure of cystathionine beta-lyase from Arabidopsis and its substrate specificity. Plant Physiol. (2001)

Release Date

2001-04-04

Peptides

CYSTATHIONINE BETA-LYASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
A

D
C

CYSTATHIONINE BETA-LYASE