MolNFT v1 · #111125 · protein
Staphylococcal alpha-hemolysin H35A mutant monomer
4YHD: “Staphylococcal alpha-hemolysin H35A mutant monomer”. X-ray diffraction, 1 ligand (CL), 14 pockets (best druggability 0.67). MolNFT v1 #111125 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4YHD
- Type
- protein
- Length
- 1,674 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-hemolysin
- UniProt
- P09616
- Ligands
- CL
- Pockets
- 14 · best druggability 0.67
Structure
x-ray diffraction · 6 distinct chains · 4% helix, 59% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-hemolysin | protein | 281 | 4% helix, 58% strand | P09616 |
| B | Alpha-hemolysin | protein | 283 | 4% helix, 59% strand | P09616 |
| C | Alpha-hemolysin | protein | 279 | 4% helix, 59% strand | P09616 |
| D | Alpha-hemolysin | protein | 282 | 5% helix, 61% strand | P09616 |
| E | Alpha-hemolysin | protein | 268 | 4% helix, 60% strand | P09616 |
| G | Alpha-hemolysin | protein | 281 | 4% helix, 59% strand | P09616 |
Ligands and binding sites
- CL · Chloride ion · ion · 5 copies · chains A, E, B, D, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 674 | 0.67 | 0.76 | 61 | CL |
| 2 | 722 | 0.67 | 0.75 | 69 | CL |
| 3 | 201 | 0.56 | 0.80 | 33 | empty |
| 4 | 196 | 0.52 | 0.78 | 25 | empty |
| 5 | 216 | 0.51 | 0.77 | 24 | empty |
Interfaces
8 interfaces between chains.
- E–G · 507 Ų buried · 10 hydrogen bonds · protein-protein
- A–E · 464 Ų buried · 3 hydrogen bonds · protein-protein
- B–G · 434 Ų buried · 2 hydrogen bonds · protein-protein
- A–G · 427 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 414 Ų buried · 5 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 P09616
- Elsewhere: RCSB PDB 4YHD · PDBe 4YHD · UniProt P09616
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