MolNFT v1 · #30645 · protein
Avidin complexed with 8-oxodeoxyguanosine
2A5B: “Avidin complexed with 8-oxodeoxyguanosine”. X-ray diffraction, 2 ligands (8HG, NAG), 3 pockets (best druggability 0.42). MolNFT v1 #30645 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2A5B
- Type
- protein
- Length
- 248 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Avidin
- UniProt
- P02701
- Ligands
- 8HG, NAG
- Pockets
- 3 · best druggability 0.42
Structure
x-ray diffraction · 1 distinct chain · 5% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Avidin | protein | 124 | 5% helix, 52% strand | P02701 |
Ligands and binding sites
- 8HG · 2'-deoxy-8-oxoguanosine · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 123 | 0.42 | 0.75 | 17 | empty |
| 2 | 85 | 0.39 | 0.76 | 16 | 8HG |
| 3 | 50 | 0.29 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1931 Ų buried · 35 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 2 glycan (disulfide, N-glycosylation).
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 2A5B · PDBe 2A5B · UniProt P02701
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