SMTL ID : 4uox.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.09 Å

Oligo State

homo-tetramer

Ligands

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

PLP.1: 14 residues within 4Å: Chain A: S.149, G.150, T.151, F.180, H.181, G.182, E.238, D.271, V.273, Q.274, K.300 Chain B: T.331, T.332 Ligands: PUT.2 16 PLIP interactions: 10 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:F.180, A:E.238, A:V.273, A:V.273 Hydrogen bonds: A:G.150, A:T.151, A:K.300, B:T.332, B:T.332 Water bridges: A:F.180, A:E.238, B:T.330, B:T.330, B:T.331, B:G.334 pi-Stacking: A:F.180 PLP.6: 14 residues within 4Å: Chain A: T.331, 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 Ligands: PUT.7 13 PLIP interactions: 10 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:F.180, B:E.238, B:V.273 Hydrogen bonds: B:G.150, B:T.151, A:T.332, A:T.332 Water bridges: B:T.151, B:F.180, B:E.238, A:T.331 Salt bridges: B:K.300 pi-Stacking: B:F.180 PLP.9: 15 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 Ligands: PUT.10 15 PLIP interactions: 11 interactions with chain C, 4 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:T.151, C:F.180, C:E.238 pi-Stacking: C:F.180 PLP.14: 14 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, E.243, D.271, V.273, Q.274, K.300 16 PLIP interactions: 5 interactions with chain C, 11 interactions with chain D Hydrogen bonds: C:T.332, C:T.332, C:T.332, D:G.150, D:T.151, D:Q.274, D:K.300 Water bridges: C:N.148, C:G.334, D:S.149, D:T.151, D:F.180, D:E.243 Hydrophobic interactions: D:E.238, D:V.273 pi-Stacking: D:F.180

3 x PUT: 1,4-DIAMINOBUTANE(Non-covalent)

PUT.2: 8 residues within 4Å: Chain A: F.91, F.180, E.243, K.300, L.419 Chain B: Q.119, T.332 Ligands: PLP.1 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:L.419 Hydrogen bonds: B:Q.119, B:T.332 PUT.7: 9 residues within 4Å: Chain A: Q.119, T.330, T.332 Chain B: F.91, F.180, E.243, K.300, L.419 Ligands: PLP.6 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.419 Hydrogen bonds: B:K.300, A:Q.119 PUT.10: 8 residues within 4Å: Chain C: F.91, E.243, K.300 Chain D: Q.119, T.330, T.331, T.332 Ligands: PLP.9 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:Q.119, C:K.300, C:K.300

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

FMT.3: 4 residues within 4Å: Chain A: Y.143, E.316 Chain B: E.44, P.48 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.44, A:Y.143 FMT.4: 4 residues within 4Å: Chain A: G.49, E.52, Y.53 Chain B: P.326 No protein-ligand interaction detected (PLIP) FMT.11: 7 residues within 4Å: Chain B: G.206, F.207, R.208 Chain C: G.206, F.207, R.208 Ligands: FMT.12 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:G.206, C:F.207, C:R.208, B:G.206 Water bridges: C:F.207, B:F.207 FMT.12: 5 residues within 4Å: Chain B: P.205, G.206 Chain C: P.205, G.206 Ligands: FMT.11 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:G.206, B:G.206 Water bridges: C:F.207, B:F.207 FMT.15: 5 residues within 4Å: Chain A: F.207, R.208 Chain D: G.206, F.207, R.208 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:F.207, A:R.208, D:G.206 Water bridges: A:G.206, A:G.206, D:F.207 FMT.17: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: K.43, E.44, P.48 Chain B: Y.143, E.316 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.316 GOL.8: 4 residues within 4Å: Chain B: Q.358, K.362, T.432, L.433 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.358, B:Q.358, B:K.362 GOL.16: 4 residues within 4Å: Chain C: L.328 Chain D: T.195, K.198, P.199 No protein-ligand interaction detected (PLIP)

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.13: 5 residues within 4Å: Chain A: F.171 Chain B: M.201, P.202 Chain C: F.171 Chain D: M.201 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.230

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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