Research workbench
Single particle cryoem structure of a darpin-aldolase platform in complex with GFP
Analyse Single particle cryoem structure of a darpin-aldolase platform in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MWQ
- Type
- protein
- Length
- 2,873 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Darpin, muscle-type aldolase chimeric fusion; Green fluorescent protein
- EC
- 4.1.2.13
- UniProt
- P00883, P42212
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 3 distinct chains · 22% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Darpin, muscle-type aldolase chimeric fusion (EC 4.1.2.13) | protein | 493 | 40% helix, 6% strand | P00883 |
| G | Green fluorescent protein | protein | 226 | 2% helix, 40% strand | P42212 |
| J, I, H | Green fluorescent protein | protein | 225 | 4% helix, 38% strand | P42212 |
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 | 1134 | 0.86 | 0.87 | 109 | empty |
| 2 | 484 | 0.80 | 0.87 | 69 | empty |
| 3 | 431 | 0.79 | 0.87 | 67 | empty |
| 4 | 110 | 0.77 | 0.97 | 32 | empty |
| 5 | 119 | 0.77 | 0.96 | 32 | empty |
Interfaces
10 interfaces between chains.
- C–D · 1196 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1171 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 1103 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 1097 Ų buried · 12 hydrogen bonds · protein-protein
- A–G · 1039 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6MWQ · Single particle cryoEM structure of a DARPin-aldolase platform in complex with GFP · the same entry in another collection · chain H against H, TM-score 1.00
- P42212 · AlphaFold monomer V2.0 prediction for green fluorescent protein (P42212) · a predicted model of the same protein · chain I against A, TM-score 0.96
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 P00883
- Every structure of UniProt P42212
- Elsewhere: RCSB PDB 6MWQ · PDBe 6MWQ · UniProt P00883 · UniProt P42212
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