4BKA: Human EphA4 ectodomain

crystal structure of the human EphA4 ectodomain in complex with human ephrin A5. Determined by X-ray diffraction at 5.3 Å resolution. Released 3 Jul 2013.

Method: X-ray diffraction
Resolution: 5.3 Å
Organism: HOMO SAPIENS
Chains: 2
Atoms: 5,087
Mol. weight: 83.34 kDa
Released: 3 Jul 2013

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

Secondary structure: helices and β-sheets

4BKA contains 17 α-helices and 63 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: 13 helices, 55 β-strands

Element	Residues	Length	Sheet
β-strand	31-34	4	1
β-strand	46-48	3	2
β-strand	55-56	2	1
β-strand	61	1	3
β-strand	65	1	3
β-strand	70-73	4	1
β-strand	82-85	4	2
β-strand	89-90	2	2
β-strand	97-104	8	1
β-strand	119	1	4
β-strand	122-129	8	2
β-strand	143-148	6	2
β-strand	168-173	6	1
β-strand	180-187	8	2
β-strand	190	1	4
β-strand	191-201	11	1
β-strand	204	1	5
β-strand	207-209	3	6
β-strand	212-214	3	6
β-strand	217	1	5
β-strand	227-230	4	7
α-helix	231-232	2
β-strand	233	1	6
α-helix	234	1
β-strand	237-238	2	8
β-strand	244-247	4	7
β-strand	253	1	7
α-helix	254-256	3
β-strand	257	1	7
β-strand	261-262	2	8
α-helix	263	1
β-strand	266-267	2	9
β-strand	274-275	2	9
α-helix	276-277	2
β-strand	280-281	2	10
β-strand	291-292	2	10
α-helix	293-294	2
β-strand	297	1	11
β-strand	304	1	10
α-helix	308	1
β-strand	309	1	11
α-helix	310	1
β-strand	314	1	12
α-helix	324-325	2
β-strand	326	1	12
α-helix	327-332	6
β-strand	335-339	5	13
β-strand	344-348	5	13
β-strand	360-366	7	14
β-strand	386	1	13
β-strand	393	1	14
β-strand	397-400	4	13
β-strand	408-417	10	14
α-helix	424-426	3
β-strand	431-435	5	14
α-helix	439-441	3
β-strand	447-448	2	15
β-strand	452	1	16
β-strand	457	1	16
β-strand	459-461	3	15
α-helix	462-464	3
β-strand	471-478	8	17
β-strand	479-481	3	18
β-strand	489-493	5	17
β-strand	497-498	2	15
β-strand	508-511	4	18
β-strand	513-517	5	17
β-strand	528-531	4	18

Chain C: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	35-39	5	19
α-helix	45-49	5
β-strand	53-56	4	20
β-strand	61-65	5	19
β-strand	81-85	5	20
α-helix	88-93	6
β-strand	101-105	5	20
β-strand	117-121	5	19
α-helix	131-133	3
β-strand	138-146	9	20
β-strand	157-163	7	20
α-helix	164-165	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ephrin type-a receptor 4	A	protein	568	HOMO SAPIENS	P54764 (AlphaFold model)
Ephrin-A5	C	protein	180	HOMO SAPIENS	P52803 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4BKA_1 EPHRIN TYPE-A RECEPTOR 4 (chains A)
MGILPSPGMPALLSLVSLLSVLLMGCVAETGVTGSRVYPANEVTLLDSRSVQGELGWIAS
PLEGGWEEVSIMDEKNTPIRTYQVCNVMEPSQNNWLRTDWITREGAQRVYIEIKFTLRDC
NSLPGVMGTCKETFNLYYYESDNDKERFIRENQFVKIDTIAADESFTQVDIGDRIMKLNT
EIRDVGPLSKKGFYLAFQDVGACIALVSVRVFYKKCPLTVRNLAQFPDTITGADTSSLVE
VRGSCVNNSEEKDVPKMYCGADGEWLVPIGNCLCNAGHEERSGECQACKIGYYKALSTDA
TCAKCPPHSYSVWEGATSCTCDRGFFRADNDAASMPCTRPPSAPLNLISNVNETSVNLEW
SSPQNTGGRQDISYNVVCKKCGAGDPSKCRPCGSGVHYTPQQNGLKTTKVSITDLLAHTN
YTFEIWAVNGVSKYNPNPDQSVSVTVTTNQAAPSSIALVQAKEVTRYSVALAWLEPDRPN
GVILEYEVKYYEKDQNERSYRIVRTAARNTDIKGLNPLTSYVFHVRARTAAGYGDFSEPL
EVTTNTVPSRIIGDGANSTGTKHHHHHH

Sequence of entity 2 (C), FASTA

>4BKA_2 EPHRIN-A5 (chains C)
MGILPSPGMPALLSLVSLLSVLLMGCVAETGAVADRYAVYWNSSNPRFQRGDYHIDVCIN
DYLDVFCPHYEDSVPEDKTERYVLYMVNFDGYSACDHTSKGFKRWECNRPHSPNGPLKFS
EKFQLFTPFSLGFEFRPGREYFYISSAIPDNGRRSCLKLKVFVRPTNSCMKGTKHHHHHH

Primary citation

Structurally Encoded Intraclass Differences in Epha Clusters Drive Distinct Cell Responses. Seiradake, E., Schaupp, A., Del Toro Ruiz, D. et al. Nat Struct Mol Biol (2013) 20:958. DOI 10.1038/NSMB.2617 · 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
3CKH 2.8 Å, Crystal structure of Eph A4 receptor
4M4R 3.13 Å, Epha4 ectodomain complex with ephrin a5

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