Research workbench
Cryptococcus neoformans HSP90 nucleotide binding domain in complex with BUCMD00452
Analyse Cryptococcus neoformans HSP90 nucleotide binding domain in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7K9V
- Type
- protein
- Length
- 413 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HSP90-like protein
- UniProt
- J9VVA4
- Ligands
- W8V, BEN, CL
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HSP90-like protein | protein | 208 | 46% helix, 21% strand | J9VVA4 |
| B | HSP90-like protein | protein | 205 | 46% helix, 21% strand | J9VVA4 |
Ligands and binding sites
- W8V · (1,3-dihydro-2H-isoindol-2-yl)(2,4-dihydroxy-6-{[1-methyl-3-(2-methylphenyl)-1H-pyrazol-5-yl]amino}phenyl)methanone · ligand · 2 copies · chains A, B
- BEN · Benzamidine · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 941 | 0.73 | 0.77 | 76 | CL |
| 2 | 269 | 0.66 | 0.83 | 32 | W8V |
| 3 | 248 | 0.65 | 0.82 | 27 | W8V |
| 4 | 56 | 0.45 | 0.84 | 13 | BEN |
| 5 | 53 | 0.43 | 0.83 | 13 | BEN |
Interfaces
1 interface between chains.
- A–B · 611 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 7K9V · Cryptococcus neoformans Hsp90 nucleotide binding domain in complex with BUCMD00452 · 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 J9VVA4
- Elsewhere: RCSB PDB 7K9V · PDBe 7K9V · UniProt J9VVA4
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