SMTL ID : 5jr2.1 (3 other biounits)

Crystal structure of the EphA4 LBD in complex with APYd3 peptide inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

hetero-1-1-mer

Ligands

2 x HEZ: HEXANE-1,6-DIOL(Non-covalent)

HEZ.1: 5 residues within 4Å: Chain A: Y.73, I.145, R.146, D.147, K.177 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.73 Hydrogen bonds: A:D.147, A:K.177, A:K.177 Water bridges: A:R.146, A:R.146 HEZ.2: 7 residues within 4Å: Chain A: S.23, N.56, W.58, R.60, I.112, E.114, F.117 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.58, A:E.114 Hydrogen bonds: A:R.60, A:E.114 Water bridges: A:N.56, A:R.60, A:E.114

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: E.5, E.75, R.173 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.5, A:R.173 Water bridges: A:E.75, A:E.75 GOL.4: 4 residues within 4Å: Chain A: R.71, D.147, V.148, G.149 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.71, A:R.71, A:G.149 Water bridges: A:Y.101, A:Y.101 GOL.5: 2 residues within 4Å: Chain A: D.133, G.135 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.133, A:G.135

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Olson, E.J. et al., Modifications of a Nanomolar Cyclic Peptide Antagonist for the EphA4 Receptor To Achieve High Plasma Stability. Acs Med.Chem.Lett. (2016)

Release Date

2016-07-06

Peptides

Ephrin type-A receptor 4: A
APYd3 peptide: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
E

Ephrin type-A receptor 4

APYd3 peptide

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