MolNFT v1 · #161924 · protein
Cryo-EM structure of SH1 full particle.
6QT9 · Orf 25: “Cryo-EM structure of SH1 full particle.”. Electron microscopy, 20 pockets (best druggability 0.82). MolNFT v1 #161924 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6QT9
- Type
- protein
- Length
- 5,520 residues
- Chains
- 30
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Orf 25; Orf 24; Orf 31; VP12; VP13
- UniProt
- Q4KPG2, Q4KPG3, Q4KPF6
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 8 distinct chains · 10% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Orf 25 | protein | 226 | 3% helix, 41% strand | Q4KPG2 |
| C, E, F, G, H, I, J, K, L, M | Orf 25 | protein | 225 | 4% helix, 39% strand | Q4KPG2 |
| a, b, c, d, e, f, i, j, k, m, o | Orf 24 | protein | 173 | 4% helix, 29% strand | Q4KPG3 |
| g, l, n | Orf 24 | protein | 167 | 6% helix, 36% strand | Q4KPG3 |
| h | Orf 24 | protein | 175 | 6% helix, 31% strand | Q4KPG3 |
| Y | Orf 31 | protein | 135 | 12% helix, 28% strand | Q4KPF6 |
| X | VP12 | protein | 24 | 92% helix, 0% strand | — |
| W | VP13 | protein | 80 | 54% helix, 0% strand | — |
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 | 173 | 0.82 | 0.97 | 39 | empty |
| 2 | 177 | 0.82 | 0.96 | 41 | empty |
| 3 | 164 | 0.82 | 0.96 | 39 | empty |
| 4 | 171 | 0.81 | 0.96 | 40 | empty |
| 5 | 1103 | 0.81 | 0.82 | 127 | empty |
Interfaces
59 interfaces between chains.
- F–b · 1523 Ų buried · 20 hydrogen bonds · protein-protein
- C–m · 1521 Ų buried · 23 hydrogen bonds · protein-protein
- I–i · 1509 Ų buried · 18 hydrogen bonds · protein-protein
- E–c · 1473 Ų buried · 26 hydrogen bonds · protein-protein
- A–o · 1437 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 6QT9 · Cryo-EM structure of SH1 full particle. · the same entry in another collection · chain C against C, 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 Q4KPG2
- Every structure of UniProt Q4KPG3
- Every structure of UniProt Q4KPF6
- Elsewhere: RCSB PDB 6QT9 · PDBe 6QT9 · UniProt Q4KPG2 · UniProt Q4KPG3 · UniProt Q4KPF6
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