MolNFT v1 · #64624 · protein
Crystal structure of a probable acetyltransferase from staphylococcus epidermidis atcc 12228
3G8W · Lactococcal prophage PS3 protein 05: “Crystal structure of a probable acetyltransferase from staphylococcus epidermidis atcc 12228”. X-ray diffraction, 7 pockets (best druggability 0.88). MolNFT v1 #64624 on GenesisL1: 3D structure…
- PDB
- 3G8W
- Type
- protein
- Length
- 649 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lactococcal prophage PS3 protein 05
- UniProt
- Q8CPX3
- Pockets
- 7 · best druggability 0.88
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Lactococcal prophage PS3 protein 05 | protein | 162 | 35% helix, 36% strand | Q8CPX3 |
| B | Lactococcal prophage PS3 protein 05 | protein | 164 | 32% helix, 37% strand | Q8CPX3 |
| D | Lactococcal prophage PS3 protein 05 | protein | 161 | 29% helix, 38% strand | Q8CPX3 |
Ligands and binding sites
- NHE · 2-[N-cyclohexylamino]ethane sulfonic acid · additive · 12 copies · chains A, B, C, D
- FLC · Citrate anion · additive · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1108 | 0.88 | 0.89 | 113 | NHE, FLC |
| 2 | 1061 | 0.88 | 0.88 | 108 | NHE |
| 3 | 221 | 0.50 | 0.75 | 30 | empty |
| 4 | 134 | 0.47 | 0.78 | 19 | empty |
| 5 | 67 | 0.47 | 0.83 | 14 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1055 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1033 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 194 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 modified (engineered).
Compared structures
- 3G8W · Crystal structure of a probable acetyltransferase from Staphylococcus epidermidis ATCC… · 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 Q8CPX3
- Elsewhere: RCSB PDB 3G8W · PDBe 3G8W · UniProt Q8CPX3
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