Research workbench

EVH1 domain from murine homer 2B/VESL 2

Analyse EVH1 domain from murine homer 2B/VESL 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1I7A
Type: protein
Length: 415 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Homer 2B; Phe-ala-phe
UniProt: Q9QWW1
Ligands: PHE
Pockets: 3 · best druggability 0.70

Structure

x-ray diffraction · 2 distinct chains · 17% helix, 47% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Homer 2B	protein	103	17% helix, 49% strand	Q9QWW1
E	Phe-ala-phe	protein	3	0% helix, 0% strand	—

Ligands and binding sites

PHE · Phenylalanine · ligand · 3 copies · chains A, B, C, D
FLC · Citrate anion · additive · 2 copies · chains A, 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	293	0.70	0.84	32	PHE
2	87	0.32	0.74	14	empty
3	82	0.30	0.72	18	empty

Interfaces

6 interfaces between chains.

C–D · 429 Å² buried · 5 hydrogen bonds · protein-protein
A–B · 428 Å² buried · 2 hydrogen bonds · protein-protein
A–E · 266 Å² buried · 1 hydrogen bond · protein-protein
B–E · 264 Å² buried · 0 hydrogen bonds · protein-protein
A–C · 45 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

1I7A · EVH1 domain from murine homer 2B/VESL 2 · the same entry in another collection · chain E against E, TM-score 1.00
Q9QWW1 · AlphaFold monomer V2.0 prediction for homer protein homolog 2 (Q9QWW1) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 Q9QWW1
Elsewhere: RCSB PDB 1I7A · PDBe 1I7A · UniProt Q9QWW1

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