MolNFT v1 · #143586 · protein

Crystal structure of the pH-like domain from DENND3

6B3Y · Denn domain-containing protein 3: “Crystal structure of the pH-like domain from DENND3”. X-ray diffraction, 4 pockets (best druggability 0.78). MolNFT v1 #143586 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6B3Y
Type: protein
Length: 450 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Denn domain-containing protein 3
UniProt: A2RT67
Pockets: 4 · best druggability 0.78

Structure

x-ray diffraction · 2 distinct chains · 47% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Denn domain-containing protein 3	protein	225	48% helix, 25% strand	A2RT67
B	Denn domain-containing protein 3	protein	225	47% helix, 23% strand	A2RT67

Pockets

4 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	1095	0.78	0.80	94	empty
2	101	0.38	0.75	21	empty
3	58	0.34	0.77	17	empty
4	75	0.33	0.75	21	empty

Interfaces

1 interface between chains.

A–B · 658 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

6B3Y · Crystal structure of the PH-like domain from DENND3 · the same entry in another collection · chain A against A, TM-score 1.00
A2RT67 · AlphaFold monomer V2.0 prediction for denn domain-containing protein 3 (A2RT67) · a predicted model of the same protein · chain B against A, TM-score 0.98

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 A2RT67
Elsewhere: RCSB PDB 6B3Y · PDBe 6B3Y · UniProt A2RT67

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