MolNFT v1 · #162749 · protein
Dodecin from streptomyces davaonensis
6RI3: “Dodecin from streptomyces davaonensis”. X-ray diffraction, 3 pockets (best druggability 0.65). MolNFT v1 #162749 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6RI3
- Type
- protein
- Length
- 408 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dodecin
- UniProt
- K4QXP8
- Pockets
- 3 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 22% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Dodecin | protein | 68 | 22% helix, 56% strand | K4QXP8 |
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 297 | 0.65 | 0.81 | 31 | empty |
| 2 | 426 | 0.65 | 0.78 | 40 | empty |
| 3 | 300 | 0.64 | 0.80 | 34 | empty |
Interfaces
8 interfaces between chains.
- B–E · 603 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 588 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 578 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 556 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 528 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6RI3 · Dodecin from Streptomyces davaonensis · the same entry in another collection · chain A against A, 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 K4QXP8
- Elsewhere: RCSB PDB 6RI3 · PDBe 6RI3 · UniProt K4QXP8
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