Research workbench
Structure of a 16 nm protein cage designed by fusing symmetric oligomeric domains, quadruple mutant, P21212 form
Analyse Structure of a 16 nm protein cage designed by fusing symmetric oligomeric… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4QF0
- Type
- protein
- Length
- 2,646 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Non-haem bromoperoxidase bpo-A2, matrix protein 1 chimera
- EC
- 1.11.1.-
- UniProt
- P29715, P03485
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 54% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Non-haem bromoperoxidase bpo-A2, matrix protein 1 chimera (EC 1.11.1.-) | protein | 441 | 54% helix, 13% strand | P29715, P03485 |
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1179 | 0.84 | 0.85 | 118 | empty |
| 2 | 1155 | 0.84 | 0.84 | 120 | empty |
| 3 | 290 | 0.61 | 0.79 | 36 | empty |
| 4 | 307 | 0.60 | 0.78 | 43 | empty |
| 5 | 287 | 0.58 | 0.77 | 36 | empty |
Interfaces
7 interfaces between chains.
- B–E · 1117 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 933 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 931 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 925 Ų buried · 22 hydrogen bonds · protein-protein
- D–E · 922 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 4QF0 · Structure of a 16 nm protein cage designed by fusing symmetric oligomeric domains… · the same entry in another collection · chain E against E, TM-score 1.00
- P29715 · AlphaFold monomer V2.0 prediction for non-haem bromoperoxidase bpo-A2 (P29715) · a predicted model of the same protein · chain E against A, TM-score 0.63
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 4QF0 · PDBe 4QF0 · UniProt P29715 · UniProt P03485
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