Research workbench
Solution NMR structure of chimeric avidin, CHIAVD(I117Y), in the biotin bound form
Analyse Solution NMR structure of chimeric avidin, CHIAVD(I117Y), in the biotin bound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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