MolNFT v1 · #155338 · protein

Crystal structure of vicilin from corylus avellana (hazelnut)

6L4C · 48-kda glycoprotein: “Crystal structure of vicilin from corylus avellana (hazelnut)”. X-ray diffraction, 1 ligand (CU), 14 pockets (best druggability 0.70). MolNFT v1 #155338 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 6L4C
Type: protein
Length: 1,085 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 48-kda glycoprotein
UniProt: Q8S4P9
Ligands: CU
Pockets: 14 · best druggability 0.70

Structure

x-ray diffraction · 3 distinct chains · 15% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	48-kda glycoprotein	protein	359	13% helix, 42% strand	Q8S4P9
B	48-kda glycoprotein	protein	373	17% helix, 39% strand	Q8S4P9
C	48-kda glycoprotein	protein	353	17% helix, 41% strand	Q8S4P9

Ligands and binding sites

CU · Copper (II) ion · metal · 3 copies · chains A, B, C

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

Pockets

14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	287	0.70	0.84	44	empty
2	168	0.70	0.88	35	empty
3	340	0.68	0.82	59	empty
4	520	0.59	0.73	73	empty
5	113	0.55	0.83	20	empty

Interfaces

3 interfaces between chains.

A–C · 2491 Å² buried · 19 hydrogen bonds · protein-protein
A–B · 2449 Å² buried · 26 hydrogen bonds · protein-protein
B–C · 2406 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

6L4C · Crystal structure of vicilin from Corylus avellana (Hazelnut) · the same entry in another collection · chain A against A, TM-score 1.00
Q8S4P9 · AlphaFold monomer V2.0 prediction for vicilin cor a 11.0101 (Q8S4P9) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 Q8S4P9
Elsewhere: RCSB PDB 6L4C · PDBe 6L4C · UniProt Q8S4P9

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