MolNFT v1 · #68863 · protein

Structural basis for vesicle tethering by the DSL1 complex

3K8P: “Structural basis for vesicle tethering by the DSL1 complex”. X-ray diffraction, 3 pockets (best druggability 0.47). MolNFT v1 #68863 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3K8P
Type: protein
Length: 889 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DSL1; Protein transport protein SEC39
UniProt: Q6CUS2, Q12745
Pockets: 3 · best druggability 0.47

Structure

x-ray diffraction · 2 distinct chains · 71% helix, 2% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C	DSL1	protein	295	77% helix, 3% strand	Q6CUS2
D	Protein transport protein SEC39	protein	594	68% helix, 1% strand	Q12745

Pockets

3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	121	0.47	0.79	25	empty
2	158	0.46	0.76	27	empty
3	50	0.40	0.81	11	empty

Interfaces

1 interface between chains.

C–D · 1073 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 20 modified (engineered).

Compared structures

3K8P · Structural basis for vesicle tethering by the Dsl1 complex · the same entry in another collection · chain C against C, TM-score 1.00
Q12745 · AlphaFold monomer V2.0 prediction for protein transport protein SEC39 (Q12745) · a predicted model of the same protein · chain D 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 Q6CUS2
Every structure of UniProt Q12745
Elsewhere: RCSB PDB 3K8P · PDBe 3K8P · UniProt Q6CUS2 · UniProt Q12745

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