Research workbench
Srtf sortase from corynebacterium diphtheriae
Analyse Srtf sortase from corynebacterium diphtheriae in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5UUS
- Type
- protein
- Length
- 413 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Possible sortase-like protein
- UniProt
- Q6NEK1
- Ligands
- CL
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 17% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Possible sortase-like protein | protein | 208 | 16% helix, 29% strand | Q6NEK1 |
| B | Possible sortase-like protein | protein | 205 | 18% helix, 29% strand | Q6NEK1 |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 4 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
- FMT · Formic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 985 | 0.73 | 0.76 | 83 | MPD |
| 2 | 51 | 0.41 | 0.82 | 13 | empty |
| 3 | 71 | 0.38 | 0.78 | 18 | MPD |
| 4 | 70 | 0.36 | 0.77 | 18 | MPD |
Interfaces
1 interface between chains.
- A–B · 513 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 2 modified (disulfide, oxidation).
Compared structures
- 5UUS · SrtF sortase from Corynebacterium diphtheriae · 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 Q6NEK1
- Elsewhere: RCSB PDB 5UUS · PDBe 5UUS · UniProt Q6NEK1
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