Research workbench
Crystal structure of a putative thiaminase II (SE1693) from staphylococcus epidermidis atcc 12228 at 1.65 a resolution
Analyse Crystal structure of a putative thiaminase II (SE1693) from staphylococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NO6
- Type
- protein
- Length
- 914 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcriptional activator tena
- EC
- 3.5.99.2
- UniProt
- Q8CNK1
- Ligands
- SO4
- Pockets
- 11 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 74% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcriptional activator tena (EC 3.5.99.2) | protein | 235 | 72% helix, 1% strand | Q8CNK1 |
| B, C | Transcriptional activator tena (EC 3.5.99.2) | protein | 226 | 75% helix, 0% strand | Q8CNK1 |
| D | Transcriptional activator tena (EC 3.5.99.2) | protein | 227 | 74% helix, 0% strand | Q8CNK1 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains C
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 7 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 6 copies · chains A, B, D, C
- IMD · Imidazole · additive · 4 copies · chains A, B, C, D
- MRD · (4R)-2-methylpentane-2,4-diol · additive · 3 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 925 | 0.84 | 0.86 | 98 | ACT, MPD, MRD |
| 2 | 364 | 0.77 | 0.87 | 28 | IMD, SO4 |
| 3 | 233 | 0.73 | 0.87 | 26 | IMD, MRD, MPD |
| 4 | 302 | 0.68 | 0.82 | 34 | ACT |
| 5 | 308 | 0.65 | 0.80 | 36 | IMD, MPD |
Interfaces
6 interfaces between chains.
- A–B · 1200 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1176 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 698 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 654 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 171 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 44 modified (engineered).
Compared structures
- 3NO6 · Crystal structure of a putative thiaminase II (SE1693) from Staphylococcus epidermidis… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8CNK1 · AlphaFold monomer V2.0 prediction for aminopyrimidine aminohydrolase (Q8CNK1) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q8CNK1
- Elsewhere: RCSB PDB 3NO6 · PDBe 3NO6 · UniProt Q8CNK1
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