MolNFT v1 · #33130 · protein

VPS36 N-terminal pH domain

2CAY · Vacuolar protein sorting protein 36: “VPS36 N-terminal pH domain”. X-ray diffraction, 1 ligand (SO4), 1 pocket (best druggability 0.46). MolNFT v1 #33130 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2CAY
Type: protein
Length: 263 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Vacuolar protein sorting protein 36
UniProt: Q06696
Ligands: SO4
Pockets: 1 · best druggability 0.46

Structure

x-ray diffraction · 2 distinct chains · 19% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Vacuolar protein sorting protein 36	protein	132	20% helix, 39% strand	Q06696
B	Vacuolar protein sorting protein 36	protein	131	19% helix, 38% strand	Q06696

Ligands and binding sites

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

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	213	0.46	0.73	31	empty

Interfaces

1 interface between chains.

A–B · 689 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

2CAY · Vps36 N-terminal PH domain · the same entry in another collection · chain A against A, TM-score 1.00
Q06696 · AlphaFold monomer V2.0 prediction for vacuolar protein-sorting- associated protein 36… · a predicted model of the same protein · chain A against A, TM-score 0.93

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 Q06696
Elsewhere: RCSB PDB 2CAY · PDBe 2CAY · UniProt Q06696

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