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Crystal structure of EPHB3

Analyse Crystal structure of EPHB3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3ZFY
Type: protein
Length: 515 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ephrin type-B receptor 3
EC: 2.7.10.1
UniProt: P54753
Pockets: 5 · best druggability 0.66

Structure

x-ray diffraction · 2 distinct chains · 42% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ephrin type-B receptor 3 (EC 2.7.10.1)	protein	260	42% helix, 13% strand	P54753
B	Ephrin type-B receptor 3 (EC 2.7.10.1)	protein	255	42% helix, 13% strand	P54753

Pockets

5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	390	0.66	0.80	48	empty
2	254	0.58	0.78	29	empty
3	217	0.56	0.79	31	empty
4	66	0.47	0.84	13	empty
5	65	0.37	0.79	14	empty

Interfaces

1 interface between chains.

A–B · 449 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

3ZFY · Crystal structure of EphB3 · the same entry in another collection · chain A against A, TM-score 1.00
P54753 · AlphaFold monomer V2.0 prediction for ephrin type-B receptor 3 (P54753) · a predicted model of the same protein · chain B against A, TM-score 0.94

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 P54753
Elsewhere: RCSB PDB 3ZFY · PDBe 3ZFY · UniProt P54753

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