MolNFT v1 · #83212 · protein
Crystal structure of myova-gtd
3WB8 · Unconventional myosin-va: “Crystal structure of myova-gtd”. X-ray diffraction, 20 pockets (best druggability 0.82). MolNFT v1 #83212 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3WB8
- Type
- protein
- Length
- 2,861 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Unconventional myosin-va
- UniProt
- Q99104
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 7 distinct chains · 65% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Unconventional myosin-va | protein | 362 | 65% helix, 1% strand | Q99104 |
| B | Unconventional myosin-va | protein | 348 | 64% helix, 1% strand | Q99104 |
| C, F | Unconventional myosin-va | protein | 359 | 66% helix, 1% strand | Q99104 |
| D | Unconventional myosin-va | protein | 360 | 65% helix, 2% strand | Q99104 |
| E | Unconventional myosin-va | protein | 361 | 66% helix, 1% strand | Q99104 |
| G | Unconventional myosin-va | protein | 360 | 65% helix, 2% strand | Q99104 |
| H | Unconventional myosin-va | protein | 352 | 66% helix, 0% strand | Q99104 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 22 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1018 | 0.82 | 0.83 | 96 | EDO |
| 2 | 1055 | 0.78 | 0.80 | 120 | EDO |
| 3 | 948 | 0.75 | 0.78 | 75 | EDO |
| 4 | 52 | 0.70 | 0.97 | 19 | empty |
| 5 | 167 | 0.51 | 0.78 | 27 | empty |
Interfaces
10 interfaces between chains.
- A–C · 878 Ų buried · 10 hydrogen bonds · protein-protein
- D–G · 870 Ų buried · 10 hydrogen bonds · protein-protein
- E–F · 861 Ų buried · 11 hydrogen bonds · protein-protein
- B–H · 787 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 503 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
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 Q99104
- Elsewhere: RCSB PDB 3WB8 · PDBe 3WB8 · UniProt Q99104
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