Research workbench
Single-particle reconstruction of DARP14 - a designed protein scaffold displaying ~17KDA darpin proteins
Analyse Single-particle reconstruction of DARP14 - a designed protein scaffold… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6C9K
- Type
- protein
- Length
- 4,923 residues
- Chains
- 24
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DARP14 - subunit a with darpin; DARP14 - subunit B
- UniProt
- Q9I2D8
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 6 distinct chains · 59% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, I, Q | DARP14 - subunit a with darpin | protein | 293 | 65% helix, 0% strand | — |
| B, J, R | DARP14 - subunit a with darpin | protein | 292 | 65% helix, 0% strand | — |
| C, K, S | DARP14 - subunit a with darpin | protein | 291 | 65% helix, 0% strand | — |
| D, L, T | DARP14 - subunit a with darpin | protein | 294 | 65% helix, 0% strand | — |
| E, F, G, M, N, O, U, V, W | DARP14 - subunit B | protein | 118 | 29% helix, 37% strand | Q9I2D8 |
| H, P, X | DARP14 - subunit B | protein | 117 | 28% helix, 39% strand | Q9I2D8 |
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 | 825 | 0.81 | 0.84 | 68 | empty |
| 2 | 758 | 0.80 | 0.83 | 73 | empty |
| 3 | 721 | 0.79 | 0.83 | 71 | empty |
| 4 | 685 | 0.78 | 0.83 | 65 | empty |
| 5 | 993 | 0.78 | 0.80 | 117 | empty |
Interfaces
63 interfaces between chains.
- N–X · 1311 Ų buried · 34 hydrogen bonds · protein-protein
- E–M · 1304 Ų buried · 34 hydrogen bonds · protein-protein
- M–U · 1303 Ų buried · 33 hydrogen bonds · protein-protein
- H–V · 1298 Ų buried · 32 hydrogen bonds · protein-protein
- F–P · 1295 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 6C9K · Single-Particle reconstruction of DARP14 - A designed protein scaffold displaying ~17kDa… · the same entry in another collection · chain G against G, 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 Q9I2D8
- Elsewhere: RCSB PDB 6C9K · PDBe 6C9K · UniProt Q9I2D8
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