MolNFT v1 · #122527 · protein

Crystal structure of avidin in complex with 1-desthiobiotinylpyrene

5IRW: “Crystal structure of avidin in complex with 1-desthiobiotinylpyrene”. X-ray diffraction, 2 ligands (D9P, NAG), 7 pockets (best druggability 0.67). MolNFT v1 #122527 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5IRW
Type: protein
Length: 484 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Avidin
UniProt: P02701
Ligands: D9P, NAG
Pockets: 7 · best druggability 0.67

Structure

x-ray diffraction · 1 distinct chain · 7% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Avidin	protein	121	7% helix, 50% strand	P02701

Ligands and binding sites

D9P · 1-desthiobiotinylpyrene · ligand · 4 copies · chains A, C, B, D
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B, C, D

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

Pockets

7 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	127	0.67	0.89	24	D9P
2	117	0.66	0.89	23	D9P
3	139	0.66	0.87	23	D9P
4	225	0.65	0.83	38	empty
5	116	0.64	0.87	27	D9P

Interfaces

6 interfaces between chains.

A–B · 1884 Å² buried · 32 hydrogen bonds · protein-protein
C–D · 1859 Å² buried · 31 hydrogen bonds · protein-protein
B–D · 635 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 627 Å² buried · 6 hydrogen bonds · protein-protein
B–C · 150 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide, 4 glycan (disulfide, N-glycosylation).

Compared structures

5IRW · Crystal structure of avidin in complex with 1-desthiobiotinylpyrene · the same entry in another collection · chain A against A, TM-score 1.00
P02701 · AlphaFold monomer V2.0 prediction for avidin (P02701) · a predicted model of the same protein · chain A 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 P02701
Elsewhere: RCSB PDB 5IRW · PDBe 5IRW · UniProt P02701

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.