5JR2: EphA4 LBD

Crystal structure of the EphA4 LBD in complex with APYd3 peptide inhibitor. Determined by X-ray diffraction at 1.75 Å resolution. Released 6 Jul 2016.

Method: X-ray diffraction
Resolution: 1.75 Å
Organisms: Homo sapiens, synthetic construct
Chains: 8
Atoms: 7,210
Mol. weight: 89.02 kDa
Ligands: HEZ
Released: 6 Jul 2016

Explore 5JR2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5JR2 contains 20 α-helices and 66 β-strands across 8 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, 13 β-strands

Element	Residues	Length	Sheet
α-helix	27-29	3
β-strand	30-35	6	1
α-helix	36-38	3
β-strand	46-48	3	2
β-strand	55-60	6	1
β-strand	66-73	8	1
β-strand	82-85	4	2
β-strand	89-90	2	2
β-strand	97-105	9	1
α-helix	108-110	3
β-strand	121-129	9	2
α-helix	139-141	3
β-strand	143-149	7	2
β-strand	154-158	5	1
β-strand	163-173	11	1
β-strand	180-187	8	2
β-strand	191-202	12	1

Chain B: 4 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	27-29	3
β-strand	30-35	6	3
α-helix	36-38	3
β-strand	46-48	3	4
β-strand	55-60	6	3
β-strand	66-73	8	3
β-strand	82-85	4	4
β-strand	89-90	2	4
β-strand	97-105	9	3
α-helix	108-110	3
β-strand	119	1	5
β-strand	121-129	9	4
α-helix	139-141	3
β-strand	143-149	7	4
β-strand	154-158	5	3
β-strand	163-173	11	3
β-strand	180-187	8	4
β-strand	190	1	5
β-strand	191-202	12	3

Chain C: 6 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	27-29	3
β-strand	30-35	6	6
α-helix	36-38	3
α-helix	45	1
β-strand	46-48	3	7
β-strand	55-60	6	6
α-helix	65	1
β-strand	66-72	7	6
β-strand	82-85	4	7
β-strand	89-90	2	7
β-strand	97-105	9	6
α-helix	108-110	3
β-strand	119	1	8
β-strand	121-129	9	7
α-helix	139-141	3
β-strand	143-149	7	7
β-strand	154-158	5	6
β-strand	163-173	11	6
β-strand	180-187	8	7
β-strand	190	1	8
β-strand	192-202	11	6

Chain D: 6 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	27-29	3
β-strand	30-35	6	9
α-helix	36-38	3
β-strand	46-48	3	10
β-strand	55-59	5	9
α-helix	65-66	2
β-strand	67-72	6	9
β-strand	82-85	4	10
α-helix	86-88	3
β-strand	89-90	2	10
β-strand	97-105	9	9
α-helix	108-110	3
β-strand	119	1	11
β-strand	121-129	9	10
α-helix	139-141	3
β-strand	143-149	7	10
β-strand	154-158	5	9
β-strand	163-173	11	9
β-strand	180-187	8	10
β-strand	190	1	11
β-strand	192-202	11	9

Chains E, F, G and H: 0 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	12
β-strand	10-11	2	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ephrin type-A receptor 4	A, B, C, D	protein	179	Homo sapiens	P54764 (AlphaFold model)
APYd3 peptide	E, F, G, H	protein	13	synthetic construct

Sequence of entity 1 (A, B, C, D), FASTA

>5JR2_1 Ephrin type-A receptor 4 (chains A, B, C, D)
GPGNEVTLLDSRSVQGELGWIASPLEGGWEEVSIMDEKNTPIRTYQVCNVMEPSQNNWLR
TDWITREGAQRVYIEIKFTLRDCNSLPGVMGTCKETFNLYYYESDNDKERFIRENQFVKI
DTIAADESFTQVDIGDRIMKLNTEIRDVGPLSKKGFYLAFQDVGACIALVSVRVFYKKA

Sequence of entity 2 (E, F, G, H), FASTA

>5JR2_2 APYd3 peptide (chains E, F, G, H)
XPYCVYRXSWSCX

Ligands and cofactors

ID	Name	Formula	Copies
HEZ	Hexane-1,6-diol	C6 H14 O2	6

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

Primary citation

Modifications of a Nanomolar Cyclic Peptide Antagonist for the EphA4 Receptor To Achieve High Plasma Stability. Olson, E.J., Lechtenberg, B.C., Zhao, C. et al. ACS Med Chem Lett (2016) 7:841-846. DOI 10.1021/acsmedchemlett.6b00132 · 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
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
4BK4 3.65 Å, crystal structure of the human EphA4 ectodomain

Browse structure collections

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