MolNFT v1 · #88914 · protein
Structure of a 16 nm protein cage designed by fusing symmetric oligomeric domains
4D9J · Designed 16NM tetrahedral protein cage containing non-haem…: “Structure of a 16 nm protein cage designed by fusing symmetric oligomeric domains”. X-ray diffraction, 20 pockets (best druggability 0.84). MolNFT v1 #88914 on GenesisL1…
- PDB
- 4D9J
- Type
- protein
- Length
- 5,256 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Designed 16NM tetrahedral protein cage containing non-haem bromoperoxidase bpo-A2 and…
- EC
- 1.11.1.-
- UniProt
- P29715, P03485
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | Designed 16NM tetrahedral protein cage containing non-haem bromoperoxidase bpo-A2 and matrix protein 1 (EC 1.11.1.-) | protein | 438 | 52% helix, 11% strand | P29715, P03485 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1053 | 0.84 | 0.85 | 94 | empty |
| 2 | 1154 | 0.84 | 0.85 | 119 | empty |
| 3 | 999 | 0.82 | 0.83 | 79 | empty |
| 4 | 932 | 0.81 | 0.83 | 70 | empty |
| 5 | 1099 | 0.75 | 0.78 | 90 | empty |
Interfaces
21 interfaces between chains.
- C–F · 1274 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 1062 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 1057 Ų buried · 21 hydrogen bonds · protein-protein
- G–I · 1034 Ų buried · 20 hydrogen bonds · protein-protein
- J–K · 1027 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 4D9J · Structure of a 16 nm protein cage designed by fusing symmetric oligomeric domains · the same entry in another collection · chain L against L, 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
- Every structure of UniProt P29715
- Every structure of UniProt P03485
- Elsewhere: RCSB PDB 4D9J · PDBe 4D9J · UniProt P29715 · UniProt P03485
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