3GXU: Eph receptor and ephrin complex

Crystal structure of Eph receptor and ephrin complex. Determined by X-ray diffraction at 2.5 Å resolution. Released 27 Oct 2009.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,831
Mol. weight: 36.47 kDa
Released: 27 Oct 2009

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

Secondary structure: helices and β-sheets

3GXU contains 4 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: 2 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
α-helix	8-10	3
β-strand	18-20	3	2
β-strand	27-32	6	1
β-strand	38-44	7	1
β-strand	54-57	4	2
β-strand	61-62	2	2
β-strand	69-75	7	1
β-strand	78	1	3
α-helix	80-82	3
β-strand	93-101	9	2
β-strand	115-121	7	2
β-strand	126	1	3
β-strand	139-145	7	1
β-strand	152-159	8	2
β-strand	164-172	9	1

Chain B: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	32	1	4
β-strand	36-37	2	4
β-strand	46	1	5
β-strand	50	1	5
β-strand	51-53	3	6
β-strand	60-65	6	4
β-strand	81-84	4	6
α-helix	86-89	4
β-strand	93	1	7
β-strand	100-102	3	6
β-strand	111-116	6	4
β-strand	134-138	5	6
β-strand	152	1	7
α-helix	154-159	6
β-strand	163-166	4	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ephrin type-A receptor 4	A	protein	175	Homo sapiens	P54764 (AlphaFold model)
Ephrin-B2	B	protein	143	Homo sapiens	P52799 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3GXU_1 Ephrin type-A receptor 4 (chains A)
NEVTLLDSRSVQGELGWIASPLEGGWEEVSIMDEKNTPIRTYQVCNVMEPSQNNWLRTDW
ITREGAQRVYIEIKFTLRDCNSLPGVMGTCKETFNLYYYESDNDKERFIRENQFVKIDTI
AADESFTQVDIGDRIMKLNTEIRDVGPLSKKGFYLAFQDVGACIALVSVRVFYKK

Sequence of entity 2 (B), FASTA

>3GXU_2 Ephrin-B2 (chains B)
SIVLEPIYWNSSNSKFLPGQGLVLYPQIGDKLDIICPKVDSKTVGQYEYYKVYMVDKDQA
DRCTIKKENTPLLNCAKPDQDIKFTIKFQEFSPNLWGLEFQKNKDYYIISTSNGSLEGLD
NQEGGVCQTRAMKILMKVGQDAS

Primary citation

Structural characterization of the EphA4-ephrin-B2 complex reveals new features enabling Eph-ephrin binding promiscuity. Qin, H., Noberini, R., Huan, X. et al. J Biol Chem (2009). DOI 10.1074/jbc.M109.064824 · 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
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

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