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Crystal structure of avidin

Analyse Crystal structure of avidin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3FDC
Type: protein
Length: 238 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Avidin
UniProt: P02701
Ligands: BTF
Pockets: 4 · best druggability 0.58

Structure

x-ray diffraction · 2 distinct chains · 3% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Avidin	protein	119	3% helix, 47% strand	P02701
B	Avidin	protein	119	3% helix, 50% strand	P02701

Ligands and binding sites

BTF · iron(II) tetracyano-5-(2-Oxo-hexahydro-thieno[3,4-d]imidazol-6-yl)-pentanoic acid (4'-methyl-[2,2']bipyridinyl-4-ylmethyl)-amide · ligand · 2 copies · chains A, B

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

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	150	0.58	0.83	25	BTF
2	145	0.55	0.81	23	BTF
3	50	0.35	0.80	16	empty
4	59	0.32	0.76	14	empty

Interfaces

1 interface between chains.

A–B · 1851 Å² buried · 31 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

3FDC · Crystal Structure of Avidin · 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 B against A, TM-score 0.97

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 3FDC · PDBe 3FDC · UniProt P02701

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