4M4P: EPHA4 ectodomain

Crystal structure of EPHA4 ectodomain. Determined by X-ray diffraction at 2.08 Å resolution. Released 30 Oct 2013.

Method: X-ray diffraction
Resolution: 2.08 Å
Organism: Homo sapiens
Chains: 1
Atoms: 4,214
Mol. weight: 58.28 kDa
Ligands: NAG
Released: 30 Oct 2013

Explore 4M4P in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4M4P contains 16 α-helices and 49 β-strands across 1 chain. 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: 16 helices, 49 β-strands

Element	Residues	Length	Sheet
β-strand	30-35	6	1
β-strand	46-48	3	2
β-strand	55-60	6	1
β-strand	66-72	7	1
β-strand	82-85	4	2
α-helix	86-88	3
β-strand	89-90	2	2
β-strand	97-105	9	1
α-helix	108-110	3
β-strand	119	1	3
β-strand	121-129	9	2
β-strand	143-149	7	2
α-helix	152-154	3
β-strand	156-158	3	4
β-strand	163-166	4	4
β-strand	167-173	7	1
β-strand	180-187	8	2
β-strand	190	1	3
β-strand	192-202	11	1
β-strand	203-204	2	5
α-helix	205-206	2
β-strand	207-209	3	6
β-strand	212-214	3	6
β-strand	217-218	2	5
β-strand	226-230	5	7
β-strand	232-233	2	6
α-helix	234	1
β-strand	237-248	12	7
β-strand	253	1	7
β-strand	257-262	6	7
α-helix	263	1
β-strand	266-269	4	8
β-strand	272-275	4	8
α-helix	276-277	2
β-strand	280-281	2	9
β-strand	291-292	2	9
α-helix	293-294	2
β-strand	297-298	2	10
β-strand	308-309	2	10
α-helix	310	1
β-strand	314	1	11
α-helix	324-325	2
β-strand	326	1	11
β-strand	333-340	8	12
β-strand	343-349	7	12
β-strand	361-368	8	13
β-strand	385-387	3	12
β-strand	393	1	13
β-strand	397-401	5	12
β-strand	408-416	9	13
α-helix	426-428	3
β-strand	429-435	7	13
α-helix	438-441	4
β-strand	447-452	6	14
β-strand	457-461	5	14
α-helix	462-464	3
β-strand	473-480	8	15
β-strand	489-493	5	15
β-strand	497-500	4	14
α-helix	503-504	2
β-strand	508-517	10	15
β-strand	520-521	2	15
α-helix	522-527	6
β-strand	528-531	4	15
α-helix	535-537	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ephrin type-A receptor 4	A	protein	518	Homo sapiens	P54764 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4M4P_1 Ephrin type-A receptor 4 (chains A)
APANEVTLLDSRSVQGELGWIASPLEGGWEEVSIMDEKNTPIRTYQVCNVMEPSQNNWLR
TDWITREGAQRVYIEIKFTLRDCNSLPGVMGTCKETFNLYYYESDNDKERFIRENQFVKI
DTIAADESFTQVDIGDRIMKLNTEIRDVGPLSKKGFYLAFQDVGACIALVSVRVFYKKCP
LTVRNLAQFPDTITGADTSSLVEVRGSCVNNSEEKDVPKMYCGADGEWLVPIGNCLCNAG
HEERSGECQACKIGYYKALSTDATCAKCPPHSYSVWEGATSCTCDRGFFRADNDAASMPC
TRPPSAPLNLISNVNETSVNLEWSSPQNTGGRQDISYNVVCKKCGAGDPSKCRPCGSGVH
YTPQQNGLKTTKVSITDLLAHTNYTFEIWAVNGVSKYNPNPDQSVSVTVTTNQAAPSSIA
LVQAKEVTRYSVALAWLEPDRPNGVILEYEVKYYEKDQNERSYRIVRTAARNTDIKGLNP
LTSYVFHVRARTAAGYGDFSEPLEVTTNTVPSRIIGDG

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2

Primary citation

Insights into Eph receptor tyrosine kinase activation from crystal structures of the EphA4 ectodomain and its complex with ephrin-A5. Xu, K., Tzvetkova-Robev, D., Xu, Y. et al. Proc Natl Acad Sci U S A (2013) 110:14634-14639. DOI 10.1073/pnas.1311000110 · 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
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
3CKH 2.8 Å, Crystal structure of Eph A4 receptor
4M4R 3.13 Å, Epha4 ectodomain complex with ephrin a5
4BK4 3.65 Å, crystal structure of the human EphA4 ectodomain

Browse structure collections

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