SMTL ID : 4itx.1

P113S mutant of E. coli Cystathionine beta-lyase MetC inhibited by reaction with L-Ala-P

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.61 Å

Oligo State

homo-tetramer

Ligands

4 x IN5: {1-[(3-HYDROXY-METHYL-5-PHOSPHONOOXY-METHYL-PYRIDIN-4-YLMETHYL)-AMINO]-ETHYL}-PHOSPHONIC ACID(Non-covalent)

IN5.1: 17 residues within 4Å: Chain A: C.85, G.86, A.87, Y.111, E.154, D.185, T.187, A.207, T.209, K.210, M.219, Y.338, S.339, W.340, R.372 Chain C: Y.56, R.58 18 PLIP interactions: 15 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:A.207, C:Y.56 Hydrogen bonds: A:G.86, A:A.87, A:Y.111, A:T.187, A:T.209, A:K.210, A:S.339, A:W.340, A:R.372, A:R.372, C:Y.56 Water bridges: A:S.158, A:W.340 Salt bridges: A:K.210, C:R.58 pi-Stacking: A:Y.111 IN5.3: 17 residues within 4Å: Chain B: C.85, G.86, A.87, Y.111, E.154, D.185, T.187, A.207, T.209, K.210, M.219, Y.338, S.339, W.340, R.372 Chain D: Y.56, R.58 18 PLIP interactions: 16 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: B:A.207, D:Y.56 Hydrogen bonds: B:G.86, B:A.87, B:Y.111, B:Y.111, B:T.209, B:K.210, B:S.339, B:W.340, B:W.340, B:R.372, B:R.372 Water bridges: B:S.158, B:W.340 Salt bridges: B:K.210, D:R.58 pi-Stacking: B:Y.111 IN5.5: 17 residues within 4Å: Chain A: Y.56, R.58 Chain C: C.85, G.86, A.87, Y.111, E.154, D.185, T.187, A.207, T.209, K.210, M.219, Y.338, S.339, W.340, R.372 16 PLIP interactions: 14 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:A.207, A:Y.56 Hydrogen bonds: C:G.86, C:A.87, C:Y.111, C:Y.111, C:K.210, C:S.339, C:W.340, C:R.372, C:R.372 Water bridges: C:S.158, C:W.340 Salt bridges: C:K.210, A:R.58 pi-Stacking: C:Y.111 IN5.7: 17 residues within 4Å: Chain B: Y.56, R.58 Chain D: C.85, G.86, A.87, Y.111, E.154, D.185, T.187, A.207, T.209, K.210, M.219, Y.338, S.339, W.340, R.372 20 PLIP interactions: 17 interactions with chain D, 3 interactions with chain B Hydrophobic interactions: D:A.207, B:Y.56 Hydrogen bonds: D:G.86, D:A.87, D:Y.111, D:T.187, D:T.209, D:T.209, D:K.210, D:S.339, D:W.340, D:W.340, D:R.372, D:R.372, B:Y.56 Water bridges: D:S.158, D:W.340 Salt bridges: D:K.210, B:R.58 pi-Stacking: D:Y.111

4 x CA: CALCIUM ION(Non-covalent)

CA.2: 4 residues within 4Å: Chain A: N.12, R.15 Chain D: L.333, E.344 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:E.344, H2O.3, H2O.5, H2O.7, H2O.39 CA.4: 4 residues within 4Å: Chain B: N.12, R.15 Chain C: L.333, E.344 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:E.344, H2O.12, H2O.16, H2O.17, H2O.17 CA.6: 4 residues within 4Å: Chain B: L.333, E.344 Chain C: N.12, R.15 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:E.344, H2O.19, H2O.23, H2O.24, H2O.27 CA.8: 4 residues within 4Å: Chain A: L.333, E.344 Chain D: N.12, R.15 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.344, H2O.32, H2O.36, H2O.37, H2O.37

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Soo, V.W. et al., Mechanistic and Evolutionary Insights from the Reciprocal Promiscuity of Two Pyridoxal Phosphate-dependent Enzymes. J.Biol.Chem. (2016)

Release Date

2014-12-24

Peptides

Cystathionine beta-lyase MetC: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Cystathionine beta-lyase MetC

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