MolNFT v1 · #63559 · protein
Crystal structure of avidin
3FDC: “Crystal structure of avidin”. X-ray diffraction, 1 ligand (BTF), 4 pockets (best druggability 0.58). MolNFT v1 #63559 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- 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.
| Volume (ų) | 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 Ų buried · 31 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
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
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.