MolNFT v1 · #119599 · protein
Pseudomonas aeruginosa hdah bound to 9,9,9 trifluoro-8,8-dihydroy-N- phenylnonanamide
5G10: “Pseudomonas aeruginosa hdah bound to 9,9,9 trifluoro-8,8-dihydroy-N- phenylnonanamide”. X-ray diffraction, 3 ligands (6DK, K, ZN), 3 pockets (best druggability 0.79). MolNFT v1 #119599 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5G10
- Type
- protein
- Length
- 746 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hdah
- UniProt
- Q9HXM1
- Ligands
- 6DK, K, ZN
- Pockets
- 3 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hdah | protein | 370 | 42% helix, 17% strand | Q9HXM1 |
| B | Hdah | protein | 376 | 41% helix, 17% strand | Q9HXM1 |
Ligands and binding sites
- 6DK · 9,9,9-tris(fluoranyl)-8,8-bis(oxidanyl)-~{N}-phenyl-nonanamide · ligand · 2 copies · chains A, B
- K · Potassium ion · metal · 4 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 413 | 0.79 | 0.88 | 56 | empty |
| 2 | 154 | 0.72 | 0.90 | 32 | 6DK |
| 3 | 162 | 0.69 | 0.88 | 33 | ZN, 6DK |
Interfaces
1 interface between chains.
- A–B · 2139 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 5G10 · Pseudomonas aeruginosa HDAH bound to 9,9,9 trifluoro-8,8-dihydroy-N-phenylnonanamide · the same entry in another collection · chain A against A, TM-score 1.00
- Q9HXM1 · AlphaFold monomer V2.0 prediction for histone deacetylase-like amidohydrolase (Q9HXM1) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q9HXM1
- Elsewhere: RCSB PDB 5G10 · PDBe 5G10 · UniProt Q9HXM1
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