4L0P: Human EphA3 receptor ligand binding domain

Structure of the human EphA3 receptor ligand binding domain complexed with ephrin-A5. Determined by X-ray diffraction at 2.26 Å resolution. Released 11 Jun 2014.

Method: X-ray diffraction
Resolution: 2.26 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,737
Mol. weight: 37.93 kDa
Ligands: CA
Released: 11 Jun 2014

Explore 4L0P in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4L0P contains 9 α-helices and 24 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 4 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	29-34	6	1
β-strand	45-47	3	2
β-strand	53-58	6	1
β-strand	64-71	8	1
β-strand	80-83	4	2
β-strand	87-88	2	2
β-strand	96-103	8	1
β-strand	104	1	3
α-helix	106-108	3
β-strand	117	1	4
β-strand	119-127	9	2
α-helix	137-139	3
α-helix	140	1
β-strand	141-147	7	2
β-strand	152	1	3
α-helix	154-159	6
β-strand	165-170	6	1
β-strand	178-185	8	2
β-strand	188	1	4
β-strand	189-200	12	1

Chain B: 5 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	31-35	5	5
α-helix	41-43	3
β-strand	49-52	4	6
β-strand	57-61	5	5
α-helix	62-63	2
α-helix	71-73	3
β-strand	76-82	7	6
α-helix	84-89	6
β-strand	96-102	7	6
β-strand	113-117	5	5
β-strand	135-143	9	6
β-strand	153-158	6	6
α-helix	161-164	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ephrin type-A receptor 3	A	protein	176	Homo sapiens	P29320 (AlphaFold model)
Ephrin-A5	B	protein	143	Homo sapiens	P52803 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4L0P_1 Ephrin type-A receptor 3 (chains A)
GSGEVNLLDSKTIQGELGWISYPSHGWEEISGVDEHYTPIRTYQVCNVMDHSQNNWLRTN
WVPRNSAQKIYVELKFTLRDCNSIPLVLGTCKETFNLYYMESDDDHGVKFREHQFTKIDT
IAADESFTQMDLGDRILKLNTEIREVGPVNKKGFYLAFQDVGACVALVSVRVYFKK

Sequence of entity 2 (B), FASTA

>4L0P_2 Ephrin-A5 (chains B)
GSGAVADRYAVYWNSSNPRFQRGDYHIDVCINDYLDVFCPHYEDSVPEDKTERYVLYMVN
FDGYSACDHTSKGFKRWECNRPHSPNGPLKFSEKFQLFTPFSLGFEFRPGREYFYISSAI
PDNGRRSCLKLKVFVRPTNSCMK

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	1

Water and common crystallization additives (SO4) are not listed.

Primary citation

Distinctive Structure of the EphA3/Ephrin-A5 Complex Reveals a Dual Mode of Eph Receptor Interaction for Ephrin-A5. Forse, G.J., Uson, M.L., Nasertorabi, F. et al. PLoS One (2015) 10:e0127081-e0127081. DOI 10.1371/journal.pone.0127081 · PubMed

Other PDB entries of the same protein (UniProt P29320 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2QOL 1.07 Å, Human EphA3 kinase and juxtamembrane region, Y596:Y602:S768G triple mutant
2QOD 1.15 Å, Human EphA3 kinase and juxtamembrane region, Y602F mutant
2QOF 1.2 Å, Human EphA3 kinase and juxtamembrane region, Y596F mutant
2QOK 1.2 Å, Human EphA3 kinase and juxtamembrane region, Y596F:Y602F:S768A triple mutant
2QOC 1.25 Å, Human EphA3 kinase domain, phosphorylated, AMP-PNP bound structure
2QOI 1.25 Å, Human EphA3 kinase and juxtamembrane region, Y596F:Y602F double mutant
2QOO 1.25 Å, Human EphA3 kinase and juxtamembrane region, Y596F:Y602F:Y742F triple mutant
4P5Q 1.35 Å, Human EphA3 Kinase domain in complex with quinoxaline derivatives
6IN0 1.5 Å, Crystal structure of EphA3 in complex with 18-Crown-6
2QO9 1.55 Å, Human EphA3 kinase and juxtamembrane region, phosphorylated, AMP-PNP bound
4P4C 1.6 Å, Human EphA3 Kinase domain in complex with quinoxaline derivatives
2QO2 1.6 Å, Human EphA3 kinase and juxtamembrane region, dephosphorylated, apo structure

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