MolNFT v1 · #175786 · protein
Complex structure of two rrm domains
7D1L · Embryonic developmental protein tofu-6: “Complex structure of two rrm domains”. X-ray diffraction, 4 pockets (best druggability 0.67). MolNFT v1 #175786 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7D1L
- Type
- protein
- Length
- 328 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Embryonic developmental protein tofu-6; Uncharacterized protein
- UniProt
- Q09293, O76616
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 23% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Embryonic developmental protein tofu-6 | protein | 80 | 23% helix, 41% strand | Q09293 |
| B | Embryonic developmental protein tofu-6 | protein | 82 | 22% helix, 40% strand | Q09293 |
| C, D | Uncharacterized protein | protein | 83 | 25% helix, 33% strand | O76616 |
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 339 | 0.67 | 0.81 | 41 | empty |
| 2 | 269 | 0.64 | 0.81 | 31 | empty |
| 3 | 80 | 0.36 | 0.75 | 16 | empty |
| 4 | 77 | 0.34 | 0.75 | 18 | empty |
Interfaces
5 interfaces between chains.
- A–C · 858 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 843 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 587 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 305 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 278 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 modified (engineered).
Compared structures
- 7D1L · complex structure of two RRM domains · the same entry in another collection · chain A against A, TM-score 1.00
- Q09293 · AlphaFold monomer V2.0 prediction for embryonic developmental protein tofu-6 (Q09293) · a predicted model of the same protein · chain A against A, TM-score 0.94
- O76616 · AlphaFold monomer V2.0 prediction for protein pid-3 (O76616) · a predicted model of the same protein · chain C against A, TM-score 0.86
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 Q09293
- Every structure of UniProt O76616
- Elsewhere: RCSB PDB 7D1L · PDBe 7D1L · UniProt Q09293 · UniProt O76616
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