SMTL ID : 4iyo.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-1-3-mer

Ligands

5 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 7 PLIP interactions: 2 interactions with chain B, 2 Ligand-Ligand interactions, 3 interactions with chain A Hydrogen bonds: B:N.240, S.1, S.1, A:Y.112, A:E.338 Salt bridges: B:R.60, A:R.117 SER.5: 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: NAK.6 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:E.57, A:T.61, A:T.61, A:N.240, B:Y.112, B:E.338 Salt bridges: A:R.60, B:R.117 Water bridges: B:R.117 SER.8: 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: NAK.9 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:E.57, D:T.61, D:T.61, D:N.240, C:Y.112 Salt bridges: D:R.60, C:R.117 SER.11: 8 residues within 4Å: Chain C: Y.58, R.60, T.61, N.240 Chain D: Y.112, R.117, E.338 Ligands: SER.12 10 PLIP interactions: 4 interactions with chain D, 2 interactions with chain C, 4 Ligand-Ligand interactions Hydrogen bonds: D:Y.112, D:E.338, C:N.240, S.11, S.11, S.12, S.12 Water bridges: D:R.117 Salt bridges: D:R.117, C:R.60 SER.12: 10 residues within 4Å: Chain C: Y.58 Chain D: Y.112, N.160, K.210, E.338, S.339, L.340, T.354, R.374 Ligands: SER.11 6 PLIP interactions: 4 interactions with chain D, 2 Ligand-Ligand interactions Hydrogen bonds: D:N.160, D:S.339, D:S.339, S.11, S.11 Salt bridges: D:R.374

3 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.10: 7 residues within 4Å: Chain A: A.18, R.266 Chain C: A.267, N.271, I.379, E.380, D.381 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:N.271, C:I.379, A:R.266, A:R.266 Water bridges: C:E.270 GOL.13: 5 residues within 4Å: Chain D: F.67, E.70, R.71, R.81, A.82 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:R.71, D:A.82 Water bridges: D:R.81, D:R.81, D:A.82, D:A.82

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

SO4.3: 3 residues within 4Å: Chain A: R.117, S.357 Chain B: F.237 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.117, A:R.117, A:R.121, A:R.121 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.4: 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: 2 interactions with chain B, 14 interactions with chain A Hydrophobic interactions: B:Y.58, A:Y.112, A:Y.112 Salt bridges: B:R.60, A:K.210, A:K.210, A:R.374 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:D.185

2 x NAK: AMINO-ACRYLATE(Non-covalent)

NAK.6: 10 residues within 4Å: Chain A: Y.58 Chain B: Y.112, N.160, K.210, E.338, S.339, L.340, T.354, R.374 Ligands: SER.5 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.112, A:Y.58 Hydrogen bonds: B:N.160, B:S.339 Salt bridges: B:R.374 NAK.9: 10 residues within 4Å: Chain C: Y.112, N.160, K.210, E.338, S.339, L.340, T.354, R.374 Chain D: Y.58 Ligands: SER.8 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:N.160, C:S.339 Salt bridges: C:R.374 Hydrophobic interactions: D:Y.58

1 x PYR: PYRUVIC ACID(Non-covalent)

PYR.7: 4 residues within 4Å: Chain A: R.121, R.125 Chain B: Q.234, F.237 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.237 Hydrogen bonds: A:R.125 Water bridges: A:R.125

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: A
Cystathionine gamma-lyase-like protein, LYS201A modified: BCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Cystathionine gamma-lyase-like protein

Cystathionine gamma-lyase-like protein, LYS201A modified

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