SMTL ID : 3meb.1

Structure of cytoplasmic aspartate aminotransferase from giardia lamblia

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 11 residues within 4Å: Chain A: I.36, V.56, G.57, W.155, N.213, Y.244, K.277, F.392, R.419 Ligands: PLP.2, EDO.12 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.57, A:N.213, A:Y.244 Salt bridges: A:K.277, A:R.419 SO4.3: 9 residues within 4Å: Chain A: S.127, G.128, T.129, S.274, S.276, R.285 Chain B: Y.90 Ligands: PLP.2, EDO.12 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.127, A:G.128, A:T.129, A:T.129, A:T.129, A:S.274, A:S.276 Salt bridges: A:R.285 SO4.11: 11 residues within 4Å: Chain B: I.36, V.56, G.57, W.155, N.213, Y.244, K.277, F.392, R.419 Ligands: EDO.10, PLP.13 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.57, B:N.213, B:Y.244 Salt bridges: B:K.277, B:R.419 SO4.14: 9 residues within 4Å: Chain A: Y.90 Chain B: S.127, G.128, T.129, S.274, S.276, R.285 Ligands: EDO.10, PLP.13 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.127, B:G.128, B:T.129, B:T.129, B:S.274, B:S.276, A:Y.90 Salt bridges: B:R.285

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

PLP.2: 16 residues within 4Å: Chain A: S.127, G.128, T.129, W.155, N.213, D.241, A.243, Y.244, S.274, S.276, K.277, R.285 Chain B: Y.90 Ligands: SO4.1, SO4.3, EDO.12 16 PLIP interactions: 15 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:N.213, A:A.243, A:Y.244 Hydrogen bonds: A:S.127, A:G.128, A:T.129, A:T.129, A:N.213, A:Y.244, A:S.274, A:S.276, A:K.277, B:Y.90 Salt bridges: A:R.285 pi-Stacking: A:W.155, A:W.155 PLP.13: 16 residues within 4Å: Chain A: Y.90 Chain B: S.127, G.128, T.129, W.155, N.213, D.241, A.243, Y.244, S.274, S.276, K.277, R.285 Ligands: EDO.10, SO4.11, SO4.14 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.244 Hydrogen bonds: B:S.127, B:G.128, B:T.129, B:N.213, B:S.274, B:S.276, B:K.277, A:Y.90 Salt bridges: B:R.285 pi-Stacking: B:W.155, B:W.155

14 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 7 residues within 4Å: Chain A: N.53, V.56, A.58, R.60, S.421, C.423, G.424 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.58, A:S.421, A:S.421 Water bridges: A:T.40, A:R.60 EDO.5: 8 residues within 4Å: Chain A: E.101, Q.104, F.105, G.109, K.110, D.111, A.115 Ligands: EDO.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.104, A:D.111 Water bridges: A:D.111, A:S.112 EDO.6: 6 residues within 4Å: Chain A: E.101, F.105, K.110, V.337, H.338 Ligands: EDO.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.101, A:K.110 EDO.7: 7 residues within 4Å: Chain A: F.108, S.112, K.113, A.114, R.260, V.263, D.264 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:F.108, A:A.114, A:D.264 Water bridges: A:K.113, A:K.113 EDO.8: 6 residues within 4Å: Chain A: Y.178, H.208, H.212, D.218, F.219, W.224 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.208, A:D.218, A:F.219 EDO.9: 5 residues within 4Å: Chain A: G.250, S.251, F.252, E.253, Y.347 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.252, A:E.253 Water bridges: A:G.250 EDO.10: 8 residues within 4Å: Chain A: Y.90, R.319, S.323 Chain B: L.37, W.155 Ligands: SO4.11, PLP.13, SO4.14 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.319, A:R.319, A:S.323 EDO.12: 10 residues within 4Å: Chain A: L.37, T.129, W.155 Chain B: Y.90, R.319, S.323, M.324 Ligands: SO4.1, PLP.2, SO4.3 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.319, B:R.319, B:S.323, B:S.323 EDO.15: 7 residues within 4Å: Chain B: N.53, V.56, A.58, R.60, S.421, C.423, G.424 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:A.58, B:S.421, B:S.421, B:G.424 Water bridges: B:N.53, B:N.53 EDO.16: 8 residues within 4Å: Chain B: E.101, Q.104, F.105, G.109, K.110, D.111, A.115 Ligands: EDO.17 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.104, B:D.111 Water bridges: B:S.112, B:S.112 EDO.17: 5 residues within 4Å: Chain B: E.101, F.105, K.110, H.338 Ligands: EDO.16 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.101, B:K.110 EDO.18: 7 residues within 4Å: Chain B: F.108, S.112, K.113, A.114, R.260, V.263, D.264 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:F.108, B:A.114 Water bridges: B:K.113 EDO.19: 6 residues within 4Å: Chain B: Y.178, H.208, H.212, D.218, F.219, W.224 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.178, B:H.208, B:D.218, B:F.219 Water bridges: B:H.212 EDO.20: 4 residues within 4Å: Chain B: S.251, F.252, E.253, Y.347 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.250, B:F.252, B:E.253

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Abendroth, J. et al., Structures of aspartate aminotransferases from Trypanosoma brucei, Leishmania major and Giardia lamblia. Acta Crystallogr F Struct Biol Commun (2015)

Release Date

2010-04-21

Peptides

Aspartate aminotransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Aspartate aminotransferase