SMTL ID : 6cja.1

Crystal structure of Cystathionine beta-lyase from Legionella pneumophila Philadelphia 1 in complex with Alanyl-PLP and Serine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-tetramer

Ligands

4 x F0G: (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-alanine(Non-covalent)

F0G.1: 20 residues within 4Å: Chain A: S.84, G.85, M.86, I.89, Y.109, E.153, N.157, D.182, T.184, F.185, S.204, T.206, K.207, S.217, S.336, L.337, T.351, R.371 Chain B: Y.55, R.57 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.109, A:Y.109 Hydrogen bonds: A:G.85, A:M.86, A:N.157, A:S.204, A:K.207, A:S.336 Salt bridges: A:K.207, A:K.207, A:R.371, B:R.57 F0G.5: 20 residues within 4Å: Chain A: Y.55, R.57 Chain B: S.84, G.85, M.86, I.89, Y.109, E.153, N.157, D.182, T.184, F.185, S.204, T.206, K.207, S.217, S.336, L.337, T.351, R.371 17 PLIP interactions: 15 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Y.109, B:Y.109 Hydrogen bonds: B:S.84, B:G.85, B:M.86, B:N.157, B:T.184, B:S.204, B:T.206, B:K.207, B:S.217, B:S.336, A:Y.55 Salt bridges: B:K.207, B:K.207, B:R.371, A:R.57 F0G.7: 20 residues within 4Å: Chain C: S.84, G.85, M.86, I.89, Y.109, E.153, N.157, D.182, T.184, F.185, S.204, T.206, K.207, S.217, S.336, L.337, T.351, R.371 Chain D: Y.55, R.57 16 PLIP interactions: 15 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:Y.109, C:Y.109 Hydrogen bonds: C:S.84, C:G.85, C:M.86, C:N.157, C:T.184, C:S.204, C:T.206, C:K.207, C:S.217, C:S.336 Salt bridges: C:K.207, C:K.207, C:R.371, D:R.57 F0G.10: 21 residues within 4Å: Chain C: Y.55, R.57 Chain D: S.84, G.85, M.86, I.89, Y.109, E.153, N.157, D.182, T.184, F.185, S.204, T.206, K.207, S.217, E.335, S.336, L.337, T.351, R.371 15 PLIP interactions: 13 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:Y.109, D:Y.109 Hydrogen bonds: D:G.85, D:M.86, D:N.157, D:S.204, D:S.204, D:S.204, D:K.207, D:S.336, C:Y.55 Salt bridges: D:K.207, D:K.207, D:R.371, C:R.57

4 x SER: SERINE(Non-covalent)

SER.2: 10 residues within 4Å: Chain A: Y.109, R.114, E.335, M.350, T.351 Chain B: E.54, Y.55, R.57, T.58, N.237 9 PLIP interactions: 2 Ligand-Ligand interactions, 3 interactions with chain B, 4 interactions with chain A Hydrogen bonds: S.2, S.2, B:T.58, B:N.237, A:Y.109, A:M.350 Salt bridges: B:R.57, A:R.114 Water bridges: A:R.114 SER.4: 10 residues within 4Å: Chain A: E.54, Y.55, R.57, T.58, N.237 Chain B: Y.109, R.114, E.335, M.350, T.351 10 PLIP interactions: 6 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:E.54, A:T.58, A:T.58, A:T.58, A:N.237, B:Y.109, B:M.350 Salt bridges: A:R.57, B:R.114 Water bridges: B:R.114 SER.8: 10 residues within 4Å: Chain C: Y.109, R.114, E.335, M.350, T.351 Chain D: E.54, Y.55, R.57, T.58, N.237 11 PLIP interactions: 4 interactions with chain C, 6 interactions with chain D, 1 Ligand-Ligand interactions Hydrogen bonds: C:Y.109, C:M.350, D:E.54, D:T.58, D:T.58, D:T.58, D:N.237 Water bridges: C:R.114, S.8 Salt bridges: C:R.114, D:R.57 SER.11: 9 residues within 4Å: Chain C: E.54, R.57, T.58, N.237 Chain D: Y.109, R.114, E.335, M.350, T.351 10 PLIP interactions: 5 interactions with chain D, 2 Ligand-Ligand interactions, 3 interactions with chain C Hydrogen bonds: D:Y.109, D:M.350, S.11, S.11, C:T.58, C:N.237 Water bridges: D:R.114, D:A.353 Salt bridges: D:R.114, C:R.57

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: K.43, Q.44, I.45, H.50, L.51 Chain D: G.30 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.43, A:K.43, A:I.45, A:L.51 Water bridges: A:H.50, A:Y.53 GOL.6: 6 residues within 4Å: Chain B: K.43, Q.44, I.45, H.50, L.51 Chain C: G.30 7 PLIP interactions: 1 interactions with chain C, 6 interactions with chain B Water bridges: C:K.27, B:H.50, B:Y.53 Hydrogen bonds: B:K.43, B:K.43, B:I.45, B:L.51 GOL.9: 3 residues within 4Å: Chain C: E.319, D.320, R.323 3 PLIP interactions: 3 interactions with chain C Water bridges: C:S.317, C:D.320, C:D.320

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Abendroth, J. et al., Crystal structure of Cystathionine beta-lyase from Legionella pneumophila Philadelphia 1 in complex with Alanyl-PLP and Serine. to be published

Release Date

2018-03-21

Peptides

Cystathionine beta-lyase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Cystathionine beta-lyase

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