MolNFT v1 · #44682 · protein
Solution NMR structure of chimeric avidin, CHIAVD(I117Y), in the biotin bound form
2MF6 · Avidin, avidin-related protein 4/5: “Solution NMR structure of chimeric avidin, CHIAVD(I117Y), in the biotin bound form”. Solution nmr, 7 pockets (best druggability 0.63). MolNFT v1 #44682 on GenesisL1: 3D structure, binding sites…
- PDB
- 2MF6
- Type
- protein
- Length
- 516 residues
- Chains
- 4
- Method
- solution nmr
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Avidin, avidin-related protein 4/5
- UniProt
- P02701, P56734
- Pockets
- 7 · best druggability 0.63
Structure
solution nmr · 1 distinct chain · 5% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, B, C | Avidin, avidin-related protein 4/5 | protein | 129 | 5% helix, 47% strand | P02701, P56734 |
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 122 | 0.63 | 0.87 | 28 | empty |
| 2 | 115 | 0.61 | 0.86 | 30 | empty |
| 3 | 113 | 0.60 | 0.86 | 29 | empty |
| 4 | 111 | 0.59 | 0.85 | 28 | empty |
| 5 | 180 | 0.52 | 0.78 | 25 | empty |
Interfaces
6 interfaces between chains.
- A–D · 1803 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 1799 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 721 Ų buried · 5 hydrogen bonds · protein-protein
- D–B · 721 Ų buried · 4 hydrogen bonds · protein-protein
- D–C · 228 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 2MF6 · Solution NMR structure of Chimeric Avidin, ChiAVD(I117Y), in the biotin bound form · the same entry in another collection · chain A against A, TM-score 1.00
- P56734 · AlphaFold monomer V2.0 prediction for avidin-related protein 4/5 (P56734) · a predicted model of the same protein · chain B against A, TM-score 0.92
- P02701 · AlphaFold monomer V2.0 prediction for avidin (P02701) · a predicted model of the same protein · chain B against A, TM-score 0.89
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
- Every structure of UniProt P56734
- Elsewhere: RCSB PDB 2MF6 · PDBe 2MF6 · UniProt P02701 · UniProt P56734
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