MolNFT v1 · #108377 · protein

Structure of the EPHA4 lbd in complex with peptide

4W50 · Ephrin type-a receptor 4: “Structure of the EPHA4 lbd in complex with peptide”. X-ray diffraction, 6 pockets (best druggability 0.77). MolNFT v1 #108377 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4W50
Type: protein
Length: 754 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ephrin type-a receptor 4; Apy peptide
EC: 2.7.10.1
UniProt: P54764
Pockets: 6 · best druggability 0.77

Structure

x-ray diffraction · 3 distinct chains · 3% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Ephrin type-a receptor 4 (EC 2.7.10.1)	protein	177	3% helix, 51% strand	P54764
C, D	Ephrin type-a receptor 4 (EC 2.7.10.1)	protein	176	3% helix, 49% strand	P54764
E, F, G, H	Apy peptide	protein	12	0% helix, 0% strand	—

Ligands and binding sites

GOL · Glycerol · additive · 6 copies · chains A, B, C, D
BU2 · 1,3-butanediol · additive · 4 copies · chains A, D, B, C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1129	0.77	0.79	120	BU2, GOL
2	545	0.71	0.80	66	BU2
3	58	0.49	0.85	13	GOL
4	58	0.46	0.84	13	GOL
5	52	0.44	0.83	15	GOL

Interfaces

10 interfaces between chains.

B–F · 635 Å² buried · 6 hydrogen bonds · protein-protein
A–E · 634 Å² buried · 7 hydrogen bonds · protein-protein
D–H · 612 Å² buried · 6 hydrogen bonds · protein-protein
C–G · 611 Å² buried · 5 hydrogen bonds · protein-protein
A–D · 597 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide (disulfide).

Compared structures

4W50 · Structure of the EphA4 LBD in complex with peptide · the same entry in another collection · chain H against H, TM-score 1.00
P54764 · AlphaFold monomer V2.0 prediction for ephrin type-a receptor 4 (P54764) · a predicted model of the same protein · chain C against A, TM-score 0.90

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P54764
Elsewhere: RCSB PDB 4W50 · PDBe 4W50 · UniProt P54764

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