MolNFT v1 · #41214 · protein
Circular permutant of avidin
2JGS: “Circular permutant of avidin”. X-ray diffraction, 1 ligand (BTN), 6 pockets (best druggability 0.67). MolNFT v1 #41214 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2JGS
- Type
- protein
- Length
- 450 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Circular permutant of avidin
- Ligands
- BTN
- Pockets
- 6 · best druggability 0.67
Structure
x-ray diffraction · 4 distinct chains · 5% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Circular permutant of avidin | protein | 109 | 6% helix, 53% strand | — |
| B | Circular permutant of avidin | protein | 116 | 5% helix, 52% strand | — |
| C | Circular permutant of avidin | protein | 112 | 5% helix, 52% strand | — |
| D | Circular permutant of avidin | protein | 113 | 5% helix, 52% strand | — |
Ligands and binding sites
- BTN · Biotin · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 422 | 0.67 | 0.80 | 44 | empty |
| 2 | 340 | 0.65 | 0.80 | 48 | empty |
| 3 | 104 | 0.65 | 0.88 | 19 | BTN |
| 4 | 100 | 0.64 | 0.88 | 18 | BTN |
| 5 | 106 | 0.62 | 0.87 | 18 | BTN |
Interfaces
6 interfaces between chains.
- A–D · 1854 Ų buried · 34 hydrogen bonds · protein-protein
- B–C · 1851 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 635 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 625 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 165 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 2JGS · Circular permutant of avidin · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 2JGS · PDBe 2JGS
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