3CKH: Eph A4 receptor

Crystal structure of Eph A4 receptor. Determined by X-ray diffraction at 2.8 Å resolution. Released 23 Sept 2008.

Method: X-ray diffraction
Resolution: 2.8 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,824
Mol. weight: 41.69 kDa
Released: 23 Sept 2008

Explore 3CKH in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3CKH contains 8 α-helices and 27 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, 14 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
α-helix	8-10	3
β-strand	18-20	3	2
β-strand	27-30	4	1
β-strand	40-45	6	1
β-strand	54-57	4	2
β-strand	61-62	2	2
β-strand	69-77	9	1
β-strand	78	1	3
α-helix	80-82	3
β-strand	93-101	9	2
α-helix	111-113	3
β-strand	115-121	7	2
β-strand	126	1	3
α-helix	135-137	3
β-strand	139-145	7	1
β-strand	152-159	8	2
β-strand	163-173	11	1

Chain B: 4 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	4
α-helix	8-10	3
β-strand	18-19	2	5
β-strand	27-30	4	4
β-strand	40-44	5	4
β-strand	54-57	4	5
β-strand	61-62	2	5
β-strand	69-77	9	4
α-helix	80-82	3
β-strand	94-101	8	5
α-helix	111-113	3
α-helix	114	1
β-strand	115-120	6	5
β-strand	126-129	4	4
β-strand	136-145	10	4
β-strand	152-159	8	5
β-strand	164-173	10	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ephrin type-A receptor 4	A, B	protein	181	Homo sapiens	P54764 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>3CKH_1 Ephrin type-A receptor 4 (chains A, B)
NEVTLLDSRSVQGELGWIASPLEGGWEEVSIMDEKNTPIRTYQVCNVMEPSQNNWLRTDW
ITREGAQRVYIEIKFTLRDCNSLPGVMGTCKETFNLYYYESDNDKERFIRENQFVKIDTI
AADESFTQVDIGDRIMKLNTEIRDVGPLSKKGFYLAFQDVGACIALVSVRVFYKKAPLTV
R

Primary citation

Crystal Structure and NMR Binding Reveal That Two Small Molecule Antagonists Target the High Affinity Ephrin-binding Channel of the EphA4 Receptor. Qin, H., Shi, J., Noberini, R. et al. J Biol Chem (2008) 283:29473-29484. DOI 10.1074/jbc.M804114200 · PubMed

Other PDB entries of the same protein (UniProt P54764 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7OFV 1.43 Å, NMR-guided design of potent and selective EphA4 agonistic ligands
5JR2 1.75 Å, Crystal structure of the EphA4 LBD in complex with APYd3 peptide inhibitor
2WO1 1.85 Å, Crystal Structure of the EphA4 Ligand Binding Domain
4M4P 2.08 Å, Crystal structure of EPHA4 ectodomain
2WO3 2.35 Å, Crystal Structure of the EphA4-ephrinA2 complex
4W4Z 2.41 Å, Structure of the EphA4 LBD in complex with peptide
4W50 2.42 Å, Structure of the EphA4 LBD in complex with peptide
2WO2 2.45 Å, Crystal Structure of the EphA4-ephrinB2 complex
3GXU 2.5 Å, Crystal structure of Eph receptor and ephrin complex
9CY8 2.5 Å, Constrained b-hairpins targeting the EphA4 ligand binding domain
4M4R 3.13 Å, Epha4 ectodomain complex with ephrin a5
4BK4 3.65 Å, crystal structure of the human EphA4 ectodomain

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