SMTL ID : 3zzj.1

Structure of an engineered aspartate aminotransferase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

2 x PLP: PYRIDOXAL-5'-PHOSPHATE(Covalent)

PLP.1: 15 residues within 4Å: Chain A: G.102, G.103, T.104, W.130, H.133, H.178, N.183, D.211, A.213, S.243, S.245, K.246, R.254 Chain B: Y.65 Ligands: PEG.5 17 PLIP interactions: 15 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:W.130, A:W.130, A:N.183, A:A.213, A:K.246 Hydrogen bonds: A:G.103, A:T.104, A:T.104, A:N.183, A:S.243, A:S.243, A:S.245, A:K.246, B:Y.65 Salt bridges: A:K.246, A:R.254 Water bridges: B:N.285 PLP.12: 15 residues within 4Å: Chain A: Y.65 Chain B: G.102, G.103, T.104, W.130, H.133, H.178, N.183, D.211, A.213, S.243, S.245, K.246, R.254 Ligands: PEG.16 16 PLIP interactions: 1 interactions with chain A, 15 interactions with chain B Water bridges: A:N.285 Hydrophobic interactions: B:W.130, B:W.130, B:N.183, B:A.213, B:K.246 Hydrogen bonds: B:G.103, B:T.104, B:T.104, B:T.104, B:N.183, B:S.243, B:S.243, B:S.245 Salt bridges: B:K.246, B:R.254

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

SO4.2: 3 residues within 4Å: Chain A: K.121, R.122, Q.170 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.122 Salt bridges: A:R.122 SO4.3: 4 residues within 4Å: Chain A: R.219, R.315, Q.316, Q.319 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.316 Water bridges: A:R.219 Salt bridges: A:R.315 SO4.13: 3 residues within 4Å: Chain B: K.121, R.122, Q.170 2 PLIP interactions: 2 interactions with chain B Water bridges: B:R.122 Salt bridges: B:R.122 SO4.14: 4 residues within 4Å: Chain B: R.219, R.315, Q.316, Q.319 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.316 Water bridges: B:R.219 Salt bridges: B:R.315

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

PEG.4: 4 residues within 4Å: Chain A: I.71, P.72, E.73, R.76 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.73, A:R.76 PEG.5: 9 residues within 4Å: Chain A: I.13, Q.33, G.34, W.130, N.183, K.246, F.348, R.374 Ligands: PLP.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.183, A:K.246, A:R.374, A:R.374 PEG.15: 4 residues within 4Å: Chain B: I.71, P.72, E.73, R.76 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.73, B:R.76 PEG.16: 9 residues within 4Å: Chain B: I.13, Q.33, G.34, W.130, N.183, K.246, F.348, R.374 Ligands: PLP.12 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.183, B:K.246, B:K.246, B:R.374, B:R.374

2 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)

BME.6: 4 residues within 4Å: Chain A: E.73, C.77, E.80, L.298 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.73 BME.17: 4 residues within 4Å: Chain B: E.73, C.77, E.80, L.298 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.73

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 3 residues within 4Å: Chain A: Y.55, N.300, L.303 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.300 Water bridges: A:N.300 GOL.8: 4 residues within 4Å: Chain A: I.68, S.273, Y.280 Chain B: D.11 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.273, B:D.11 Water bridges: A:A.277, A:A.281 GOL.9: 2 residues within 4Å: Chain A: Q.323, N.327 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.327 GOL.10: 4 residues within 4Å: Chain A: A.115, K.116, N.117, T.118 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.115 GOL.11: 3 residues within 4Å: Chain A: N.138, L.142, E.143 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.138, A:N.138 GOL.18: 3 residues within 4Å: Chain B: Y.55, N.300, L.303 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.300 Water bridges: B:N.300 GOL.19: 4 residues within 4Å: Chain A: D.11 Chain B: I.68, S.273, Y.280 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:D.11, B:S.273 Water bridges: B:A.277, B:A.281 GOL.20: 2 residues within 4Å: Chain B: Q.323, N.327 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.327 GOL.21: 4 residues within 4Å: Chain B: A.115, K.116, N.117, T.118 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.115 GOL.22: 3 residues within 4Å: Chain B: N.138, L.142, E.143 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.138, B:N.138

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fernandez, F.J. et al., Structure and Mechanism of a Cysteine Sulfinate Desulfinase Engineered on the Aspartate Aminotransferase Scaffold. Biocim.Biophys.Acta (2011)

Release Date

2011-12-28

Peptides

ASPARTATE AMINOTRANSFERASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

ASPARTATE AMINOTRANSFERASE

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