MolNFT v1 · #127931 · protein

Structure of vwc domain from CCN3

5NB8 · Protein nov homolog: “Structure of vwc domain from CCN3”. X-ray diffraction, 1 pocket (best druggability 0.58). MolNFT v1 #127931 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5NB8
Type: protein
Length: 280 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein nov homolog
UniProt: Q9QZQ5
Pockets: 1 · best druggability 0.58

Structure

x-ray diffraction · 1 distinct chain · 0% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Protein nov homolog	protein	70	0% helix, 46% strand	Q9QZQ5

Ligands and binding sites

IMD · Imidazole · additive · 5 copies · chains A, B, C, D
GOL · Glycerol · additive · chains B, C

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	369	0.58	0.76	46	IMD, GOL

Interfaces

4 interfaces between chains.

A–B · 805 Å² buried · 11 hydrogen bonds · protein-protein
C–D · 766 Å² buried · 10 hydrogen bonds · protein-protein
B–C · 287 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 233 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 20 disulfide (disulfide).

Compared structures

5NB8 · Structure of vWC domain from CCN3 · the same entry in another collection · chain D against D, TM-score 1.00
Q9QZQ5 · AlphaFold monomer V2.0 prediction for ccn family member 3 (Q9QZQ5) · a predicted model of the same protein · chain A against A, TM-score 0.91

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 Q9QZQ5
Elsewhere: RCSB PDB 5NB8 · PDBe 5NB8 · UniProt Q9QZQ5

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