MolNFT v1 · #122525 · protein

Crystal structure of avidin in complex with 1-biotinylpyrene

5IRU: “Crystal structure of avidin in complex with 1-biotinylpyrene”. X-ray diffraction, 2 ligands (B9P, NAG), 7 pockets (best druggability 0.68). MolNFT v1 #122525 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5IRU
Type: protein
Length: 488 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Avidin
UniProt: P02701
Ligands: B9P, NAG
Pockets: 7 · best druggability 0.68

Structure

x-ray diffraction · 3 distinct chains · 7% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Avidin	protein	121	7% helix, 50% strand	P02701
B, C	Avidin	protein	122	7% helix, 49% strand	P02701
D	Avidin	protein	123	7% helix, 49% strand	P02701

Ligands and binding sites

B9P · 1-biotinylpyrene · 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	139	0.68	0.89	23	B9P
2	209	0.66	0.85	36	empty
3	141	0.66	0.87	24	B9P
4	154	0.65	0.86	24	B9P
5	168	0.63	0.84	28	B9P

Interfaces

6 interfaces between chains.

A–B · 1858 Å² buried · 37 hydrogen bonds · protein-protein
C–D · 1830 Å² buried · 39 hydrogen bonds · protein-protein
B–D · 653 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 641 Å² buried · 5 hydrogen bonds · protein-protein
B–C · 151 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

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

Compared structures

5IRU · Crystal structure of avidin in complex with 1-biotinylpyrene · the same entry in another collection · chain D against D, 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 5IRU · PDBe 5IRU · UniProt P02701

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