MolNFT v1 · #58332 · protein
Crystal structure of octameric pore form of gamma-hemolysin from staphylococcus aureus
3B07 · Gamma-hemolysin component B: “Crystal structure of octameric pore form of gamma-hemolysin from staphylococcus aureus”. X-ray diffraction, 20 pockets (best druggability 0.80). MolNFT v1 #58332 on GenesisL1: 3D structure, binding…
- PDB
- 3B07
- Type
- protein
- Length
- 2,216 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gamma-hemolysin component B; Gamma-hemolysin component a
- UniProt
- Q931F3, P0A071
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 66% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Gamma-hemolysin component B | protein | 284 | 4% helix, 63% strand | Q931F3 |
| B, D, F, H | Gamma-hemolysin component a | protein | 270 | 4% helix, 68% strand | P0A071 |
Ligands and binding sites
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 4 copies · chains A, C, E, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 880 | 0.80 | 0.83 | 108 | empty |
| 2 | 1199 | 0.78 | 0.80 | 127 | empty |
| 3 | 879 | 0.77 | 0.80 | 91 | empty |
| 4 | 851 | 0.77 | 0.81 | 86 | empty |
| 5 | 297 | 0.68 | 0.83 | 43 | empty |
Interfaces
15 interfaces between chains.
- A–H · 2463 Ų buried · 59 hydrogen bonds · protein-protein
- E–D · 2420 Ų buried · 62 hydrogen bonds · protein-protein
- G–F · 2409 Ų buried · 57 hydrogen bonds · protein-protein
- C–B · 2399 Ų buried · 61 hydrogen bonds · protein-protein
- E–F · 2079 Ų buried · 55 hydrogen bonds · protein-protein
Compared structures
- 3B07 · Crystal structure of octameric pore form of gamma-hemolysin from Staphylococcus aureus · the same entry in another collection · chain H against H, TM-score 1.00
- P0A071 · AlphaFold monomer V2.0 prediction for gamma-hemolysin component a (P0A071) · a predicted model of the same protein · chain B against A, TM-score 0.85
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 Q931F3
- Every structure of UniProt P0A071
- Elsewhere: RCSB PDB 3B07 · PDBe 3B07 · UniProt Q931F3 · UniProt P0A071
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