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Ligand binding domain of human ephrin type-B receptor 3

Analyse Ligand binding domain of human ephrin type-B receptor 3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3P1I
Type: protein
Length: 502 residues
Chains: 3
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
Ligands: SO4, CL
Pockets: 3 · best druggability 0.82

Structure

x-ray diffraction · 3 distinct chains · 4% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ephrin type-B receptor 3 (EC 2.7.10.1)	protein	171	4% helix, 47% strand	P54753
B	Ephrin type-B receptor 3 (EC 2.7.10.1)	protein	164	4% helix, 46% strand	P54753
C	Ephrin type-B receptor 3 (EC 2.7.10.1)	protein	167	4% helix, 45% strand	P54753

Ligands and binding sites

SO4 · Sulfate ion · ion · 2 copies · chains A, B
CL · Chloride ion · ion · chains B

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

Pockets

3 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	775	0.82	0.85	51	empty
2	161	0.65	0.86	27	empty
3	275	0.52	0.75	49	empty

Interfaces

3 interfaces between chains.

A–C · 732 Å² buried · 13 hydrogen bonds · protein-protein
B–C · 459 Å² buried · 5 hydrogen bonds · protein-protein
A–B · 287 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

3P1I · Ligand binding domain of human ephrin type-B receptor 3 · 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 C against A, TM-score 0.95

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 3P1I · PDBe 3P1I · UniProt P54753

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