SMTL ID : 4uoy.1

Crystal structure of YgjG in complex with Pyridoxal-5'-phosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.31 Å

Oligo State

homo-tetramer

Ligands

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

PLP.1: 14 residues within 4Å: Chain A: S.149, G.150, T.151, F.180, H.181, G.182, E.238, E.243, D.271, V.273, Q.274, K.300 Chain B: T.331, T.332 16 PLIP interactions: 13 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:F.180, A:E.238, A:V.273 Hydrogen bonds: A:G.150, A:T.151, A:E.243, A:Q.274, B:T.332 Water bridges: A:S.149, A:S.149, A:T.151, A:F.180, B:T.330, B:G.334 Salt bridges: A:K.300 pi-Stacking: A:F.180 PLP.3: 12 residues within 4Å: Chain A: T.332 Chain B: S.149, G.150, T.151, F.180, H.181, G.182, E.238, D.271, V.273, Q.274, K.300 12 PLIP interactions: 8 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:E.238, B:V.273, B:K.300 Hydrogen bonds: B:G.150, B:T.151, B:K.300, A:T.332, A:T.332 Water bridges: B:E.238, A:N.148, A:F.333 pi-Stacking: B:F.180 PLP.5: 14 residues within 4Å: Chain C: S.149, G.150, T.151, F.180, H.181, G.182, E.238, E.243, D.271, V.273, Q.274, K.300 Chain D: T.331, T.332 17 PLIP interactions: 11 interactions with chain C, 6 interactions with chain D Hydrophobic interactions: C:E.238, C:V.273 Hydrogen bonds: C:G.150, C:T.151, C:E.243, C:K.300, D:T.331, D:T.332, D:T.332, D:T.332 Water bridges: C:T.151, C:F.180, C:E.238, D:T.331, D:F.333 Salt bridges: C:K.300 pi-Stacking: C:F.180 PLP.7: 13 residues within 4Å: Chain C: T.331, T.332 Chain D: S.149, G.150, T.151, F.180, H.181, G.182, E.238, D.271, V.273, Q.274, K.300 17 PLIP interactions: 11 interactions with chain D, 6 interactions with chain C Hydrophobic interactions: D:F.180, D:E.238, D:V.273, D:V.273 Hydrogen bonds: D:G.150, D:T.151, D:Q.274, C:T.332, C:T.332, C:T.332 Water bridges: D:S.149, D:T.151, C:N.148, C:T.331, C:F.333 Salt bridges: D:K.300 pi-Stacking: D:F.180

1 x FMT: FORMIC ACID(Non-functional Binders)

FMT.2: 5 residues within 4Å: Chain A: Q.119, L.121, D.123, R.126 Chain B: F.50 No protein-ligand interaction detected (PLIP)

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: F.42, F.50 Chain B: H.117, Q.119, L.121, D.123, R.126 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.119, B:D.123, B:R.126 Water bridges: B:Q.119 GOL.6: 2 residues within 4Å: Chain B: P.202 Chain C: F.171 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cha, H.J. et al., Structure of Putrescine Aminotransferase from Escherichia Coli Provides Insights Into the Substrate Specificity Among Class III Aminotransferases. Plos One (2014)

Release Date

2014-12-10

Peptides

PUTRESCINE AMINOTRANSFERASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

PUTRESCINE AMINOTRANSFERASE

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