SMTL ID : 4kyo.1

Alanine-glyoxylate aminotransferase variant K390A in complex with the TPR domain of human Pex5p

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-2-2-mer

Ligands

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

SO4.1: 7 residues within 4Å: Chain A: Y.262, H.264, T.265 Chain B: S.83, G.84, H.85, Q.210 10 PLIP interactions: 6 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:G.84, B:H.85, B:Q.210, A:Y.262, A:T.265, A:T.265 Water bridges: B:H.85, B:H.85, A:T.265 Salt bridges: B:H.85 SO4.2: 6 residues within 4Å: Chain A: S.83, G.84, H.85, Q.210 Chain B: Y.262, T.265 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:Y.262, B:Y.262, B:T.265, A:G.84, A:H.85, A:Q.210 Water bridges: B:T.265 Salt bridges: A:H.85

2 x BTB: 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

BTB.3: 6 residues within 4Å: Chain A: K.247, W.248, N.251, D.256, Q.258, M.261 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.251, A:D.256, A:Q.258 Water bridges: A:D.245, A:W.248, A:W.248 BTB.9: 6 residues within 4Å: Chain B: K.247, W.248, N.251, D.256, Q.258, M.261 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:W.248, B:N.251, B:D.256

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

BME.4: 6 residues within 4Å: Chain A: H.157, Q.166, P.167, L.168, P.194, Q.200 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.166, A:L.168 BME.5: 4 residues within 4Å: Chain A: W.334, M.350, G.351, G.352 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.351, A:G.351 BME.6: 1 residues within 4Å: Chain A: Y.299 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.372 BME.7: 3 residues within 4Å: Chain A: P.127, M.128, T.129 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.129 BME.8: 7 residues within 4Å: Chain A: P.267, V.268, I.269, S.270 Chain B: P.216, P.217, S.270 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.267, A:I.269, A:S.270 BME.10: 7 residues within 4Å: Chain B: V.79, I.80, S.81, Y.243, L.249, W.253, H.264 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.81, B:W.253 BME.11: 4 residues within 4Å: Chain B: K.149, P.150, V.151, K.179 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.179 BME.12: 4 residues within 4Å: Chain A: S.21 Chain B: D.54, Q.57, E.61 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.54 BME.13: 6 residues within 4Å: Chain A: D.54, Q.57, I.58, E.61 Chain B: L.20, S.21 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.54 BME.14: 5 residues within 4Å: Chain B: W.334, M.350, G.351, G.352, R.362 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.362 BME.15: 4 residues within 4Å: Chain C: N.209, Y.211, L.240, Q.241 2 PLIP interactions: 2 interactions with chain C Water bridges: C:Q.36, C:Q.241 BME.16: 2 residues within 4Å: Chain D: M.96, K.216 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fodor, K. et al., Ligand-Induced Compaction of the PEX5 Receptor-Binding Cavity Impacts Protein Import Efficiency into Peroxisomes. Traffic (2015)

Release Date

2014-11-19

Peptides

Serine-pyruvate aminotransferase: AB
Peroxisomal targeting signal 1 receptor: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
B

D
D

Serine-pyruvate aminotransferase

Peroxisomal targeting signal 1 receptor

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