SMTL ID : 4iy7.1

crystal structure of cystathionine gamma lyase (XometC) from Xanthomonas oryzae pv. oryzae in complex with E-site serine, A-site external aldimine structure with serine and A-site external aldimine structure with aminoacrylate intermediates

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-tetramer

Ligands

4 x SER: SERINE(Non-covalent)

SER.1: 7 residues within 4Å: Chain A: Y.112, R.117, E.338 Chain B: Y.58, R.60, T.61, N.240 8 PLIP interactions: 4 interactions with chain A, 2 Ligand-Ligand interactions, 2 interactions with chain B Hydrogen bonds: A:Y.112, A:E.338, S.1, S.1, B:N.240 Water bridges: A:R.117 Salt bridges: A:R.117, B:R.60 SER.6: 9 residues within 4Å: Chain A: E.57, Y.58, R.60, T.61, N.240 Chain B: Y.112, R.117, E.338 Ligands: KOU.8 9 PLIP interactions: 4 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:Y.112, B:E.338, A:E.57, A:T.61, A:T.61, A:N.240 Water bridges: B:R.117 Salt bridges: B:R.117, A:R.60 SER.9: 9 residues within 4Å: Chain C: Y.112, R.117, E.338 Chain D: E.57, Y.58, R.60, T.61, N.240 Ligands: KOU.10 9 PLIP interactions: 4 interactions with chain C, 5 interactions with chain D Hydrogen bonds: C:Y.112, C:E.338, D:E.57, D:T.61, D:T.61, D:N.240 Water bridges: C:R.117 Salt bridges: C:R.117, D:R.60 SER.11: 9 residues within 4Å: Chain C: E.57, Y.58, R.60, T.61, N.240 Chain D: Y.112, R.117, E.338 Ligands: KOU.13 8 PLIP interactions: 4 interactions with chain D, 2 Ligand-Ligand interactions, 2 interactions with chain C Hydrogen bonds: D:Y.112, D:E.338, S.11, S.11, C:N.240 Water bridges: D:R.117 Salt bridges: D:R.117, C:R.60

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: D.167, I.168, A.169, L.199, R.304, Q.305 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.167, A:D.167, A:I.168, A:A.169, A:R.304 GOL.3: 5 residues within 4Å: Chain A: E.280, T.281, H.282, P.283, I.285 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.285 Water bridges: A:E.286

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

SO4.4: 4 residues within 4Å: Chain A: R.117, R.121, S.357 Chain B: F.237 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.117, A:R.117, A:S.357 Salt bridges: A:R.121

1 x 0JO: 2-{[(E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}prop-2-enoic acid(Non-covalent)

0JO.5: 21 residues within 4Å: Chain A: S.87, G.88, M.89, Y.112, E.156, N.160, D.185, T.187, F.188, S.207, T.209, K.210, V.219, G.220, E.338, S.339, L.340, T.354, R.374 Chain B: Y.58, R.60 16 PLIP interactions: 14 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:Y.112, A:Y.112, B:Y.58 Hydrogen bonds: A:S.87, A:G.88, A:M.89, A:N.160, A:S.207, A:S.207, A:K.210, A:S.339 Water bridges: A:E.156 Salt bridges: A:K.210, A:K.210, A:R.374, B:R.60

2 x PYR: PYRUVIC ACID(Non-covalent)

PYR.7: 4 residues within 4Å: Chain A: R.121, R.125 Chain B: Q.234, F.237 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:Q.234, B:F.237 Hydrogen bonds: A:R.125 Water bridges: A:R.125 Salt bridges: A:R.121 PYR.12: 5 residues within 4Å: Chain D: N.271, I.379, E.380, D.381, L.382 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain D Water bridges: B:R.266, D:G.383 Hydrogen bonds: D:N.271, D:D.381, D:L.382

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

KOU.8: 22 residues within 4Å: Chain A: Y.58, R.60 Chain B: S.87, G.88, M.89, Y.112, E.156, N.160, D.185, T.187, F.188, S.207, T.209, K.210, V.219, G.220, E.338, S.339, L.340, T.354, R.374 Ligands: SER.6 19 PLIP interactions: 15 interactions with chain B, 2 interactions with chain A, 2 Ligand-Ligand interactions Hydrophobic interactions: B:Y.112 Hydrogen bonds: B:S.87, B:G.88, B:M.89, B:Y.112, B:N.160, B:T.187, B:S.207, B:T.209, B:K.210, B:E.338, B:S.339, A:Y.58, S.6, S.6 Salt bridges: B:K.210, B:K.210, B:R.374, A:R.60 KOU.10: 22 residues within 4Å: Chain C: S.87, G.88, M.89, Y.112, E.156, N.160, D.185, T.187, F.188, S.207, T.209, K.210, V.219, G.220, E.338, S.339, L.340, T.354, R.374 Chain D: Y.58, R.60 Ligands: SER.9 19 PLIP interactions: 16 interactions with chain C, 1 interactions with chain D, 2 Ligand-Ligand interactions Hydrophobic interactions: C:Y.112 Hydrogen bonds: C:S.87, C:G.88, C:M.89, C:Y.112, C:N.160, C:T.187, C:S.207, C:T.209, C:K.210, C:E.338, C:S.339, S.9, S.9 Water bridges: C:E.156 Salt bridges: C:K.210, C:K.210, C:R.374, D:R.60 KOU.13: 22 residues within 4Å: Chain C: Y.58, R.60 Chain D: S.87, G.88, M.89, Y.112, E.156, N.160, D.185, T.187, F.188, S.207, T.209, K.210, V.219, G.220, E.338, S.339, L.340, T.354, R.374 Ligands: SER.11 15 PLIP interactions: 11 interactions with chain D, 2 Ligand-Ligand interactions, 2 interactions with chain C Hydrophobic interactions: D:Y.112 Hydrogen bonds: D:G.88, D:M.89, D:N.160, D:S.207, D:K.210, D:S.339, S.11, S.11, C:Y.58 Water bridges: D:T.115 Salt bridges: D:K.210, D:K.210, D:R.374, C:R.60

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ngo, H.P. et al., PLP undergoes conformational changes during the course of an enzymatic reaction. Acta Crystallogr.,Sect.D (2014)

Release Date

2014-01-29

Peptides

Cystathionine gamma-lyase-like protein: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Cystathionine gamma-lyase-like protein

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