MolNFT v1 · #145846 · protein
Calcarisporiella thermophila HSP104
6D00: “Calcarisporiella thermophila HSP104”. Electron microscopy, 1 ligand (ADP), 20 pockets (best druggability 0.84). MolNFT v1 #145846 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6D00
- Type
- protein
- Length
- 4,824 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Calcarisporiella thermophila HSP104
- Ligands
- ADP
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 1 distinct chain · 49% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1, 2, 3, 4, 5, 6 | Calcarisporiella thermophila HSP104 | protein | 804 | 49% helix, 8% strand | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 12 copies · chains 1, 6, 2, 3, 4, 5
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 1181 | 0.84 | 0.85 | 113 | ADP |
| 2 | 1177 | 0.84 | 0.84 | 100 | ADP |
| 3 | 1043 | 0.84 | 0.85 | 94 | ADP |
| 4 | 889 | 0.83 | 0.85 | 78 | ADP |
| 5 | 982 | 0.83 | 0.84 | 82 | ADP |
Interfaces
6 interfaces between chains.
- 1–2 · 4044 Ų buried · 60 hydrogen bonds · protein-protein
- 5–6 · 3737 Ų buried · 53 hydrogen bonds · protein-protein
- 2–3 · 3648 Ų buried · 35 hydrogen bonds · protein-protein
- 3–4 · 3620 Ų buried · 43 hydrogen bonds · protein-protein
- 4–5 · 3297 Ų buried · 41 hydrogen bonds · protein-protein
Compared structures
- 6D00 · Calcarisporiella thermophila Hsp104 · the same entry in another collection · chain 1 against 1, 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
- Elsewhere: RCSB PDB 6D00 · PDBe 6D00
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