SMTL ID : 3zzk.1

Structure of an engineered aspartate aminotransferase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.78 Å

Oligo State

homo-dimer

Ligands

2 x PMP: 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE(Non-covalent)

PMP.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: SO4.4 15 PLIP interactions: 13 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:N.183, A:A.213 Hydrogen bonds: A:G.103, A:T.104, A:W.130, A:N.183, A:S.243, A:S.245, A:K.246, B:Y.65 Water bridges: A:R.254, B:S.284 Salt bridges: A:R.254 pi-Stacking: A:W.130, A:W.130 PMP.11: 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: SO4.14 16 PLIP interactions: 14 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:N.183, B:A.213 Hydrogen bonds: B:G.103, B:T.104, B:T.104, B:W.130, B:N.183, B:S.243, B:S.245, B:K.246 Water bridges: B:R.254, A:Y.65, A:S.284 Salt bridges: B:R.254 pi-Stacking: B:W.130, B:W.130

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

SO4.2: 3 residues within 4Å: Chain A: R.315, Q.316, Q.319 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.316, A:Q.319, A:Q.319 Salt bridges: A:R.315 SO4.3: 2 residues within 4Å: Chain A: R.122, Q.170 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.122, A:R.122 Salt bridges: A:R.122 SO4.4: 8 residues within 4Å: Chain A: I.13, G.34, W.130, N.183, K.246, F.348, R.374 Ligands: PMP.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:W.130, A:N.183 Water bridges: A:K.246, A:K.246 Salt bridges: A:K.246, A:R.374 SO4.5: 4 residues within 4Å: Chain A: A.17, R.21, Q.33 Chain B: N.64 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.21, A:Q.33, B:N.64 SO4.12: 3 residues within 4Å: Chain B: R.315, Q.316, Q.319 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.316, B:Q.319, B:Q.319 Salt bridges: B:R.315 SO4.13: 2 residues within 4Å: Chain B: R.122, Q.170 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.122, B:R.122 Salt bridges: B:R.122 SO4.14: 8 residues within 4Å: Chain B: I.13, G.34, W.130, N.183, K.246, F.348, R.374 Ligands: PMP.11 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:W.130, B:N.183 Water bridges: B:K.246, B:K.246 Salt bridges: B:K.246, B:R.374 SO4.15: 4 residues within 4Å: Chain A: N.64 Chain B: A.17, R.21, Q.33 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.64, B:R.21, B:Q.33

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 4 residues within 4Å: Chain A: Y.55, T.296, N.300, L.303 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.300 Water bridges: A:K.51 GOL.7: 8 residues within 4Å: Chain A: P.128, S.129, W.130, P.131, N.183, P.184, V.370, S.372 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.372, A:S.372 Water bridges: A:S.129, A:S.129, A:S.372 GOL.8: 5 residues within 4Å: Chain A: K.134, N.138, E.143, V.144 Ligands: GOL.10 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.134, A:N.138, A:E.143, A:V.144 GOL.9: 2 residues within 4Å: Chain A: P.72, R.76 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.76, A:R.76 GOL.10: 5 residues within 4Å: Chain A: N.138, G.141, L.142, E.143 Ligands: GOL.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.138 GOL.16: 4 residues within 4Å: Chain B: Y.55, T.296, N.300, L.303 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.300 Water bridges: B:K.51 GOL.17: 8 residues within 4Å: Chain B: P.128, S.129, W.130, P.131, N.183, P.184, V.370, S.372 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.372, B:S.372 Water bridges: B:S.129, B:S.129, B:S.372 GOL.18: 5 residues within 4Å: Chain B: K.134, N.138, E.143, V.144 Ligands: GOL.20 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.134, B:N.138, B:E.143, B:E.143, B:V.144 GOL.19: 2 residues within 4Å: Chain B: P.72, R.76 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.76, B:R.76 GOL.20: 5 residues within 4Å: Chain B: N.138, G.141, L.142, E.143 Ligands: GOL.18 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: 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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