SMTL ID : 4l0p.1

Structure of the human EphA3 receptor ligand binding domain complexed with ephrin-A5

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.26 Å

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 6 residues within 4Å: Chain B: Y.12, N.14, N.17, P.40, H.41, Y.42 No protein-ligand interaction detected (PLIP)

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

SO4.2: 3 residues within 4Å: Chain A: R.111, E.112, H.113 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.112, A:H.113 Salt bridges: A:H.113 SO4.3: 2 residues within 4Å: Chain A: Y.71, K.175 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.71, A:Y.71 SO4.5: 3 residues within 4Å: Chain B: R.136, P.137, S.140 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.140 Salt bridges: B:R.136 SO4.6: 2 residues within 4Å: Chain B: R.108, R.111 5 PLIP interactions: 5 interactions with chain B Water bridges: B:E.106, B:R.108, B:R.108 Salt bridges: B:R.108, B:R.111 SO4.7: 1 residues within 4Å: Chain B: N.139 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.139

1 x CA: CALCIUM ION(Non-covalent)

CA.4: 2 residues within 4Å: Chain B: H.26, D.28 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.26, B:D.28, H2O.4

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Forse, G.J. et al., Distinctive Structure of the EphA3/Ephrin-A5 Complex Reveals a Dual Mode of Eph Receptor Interaction for Ephrin-A5. Plos One (2015)

Release Date

2014-06-11

Peptides

Ephrin type-A receptor 3: A
Ephrin-A5: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ephrin type-A receptor 3

Ephrin-A5