MolNFT v1 · #114527 · protein
Apo structure of transcriptional factor arar from bacteroides thetaiotaomicron vpi
5BS6 · Transcriptional regulator arar: “Apo structure of transcriptional factor arar from bacteroides thetaiotaomicron vpi”. X-ray diffraction, 14 pockets (best druggability 0.60). MolNFT v1 #114527 on GenesisL1: 3D structure, binding…
- PDB
- 5BS6
- Type
- protein
- Length
- 902 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcriptional regulator arar
- UniProt
- Q8AAV8
- Pockets
- 14 · best druggability 0.60
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcriptional regulator arar | protein | 223 | 31% helix, 32% strand | Q8AAV8 |
| B | Transcriptional regulator arar | protein | 225 | 30% helix, 30% strand | Q8AAV8 |
| C | Transcriptional regulator arar | protein | 226 | 32% helix, 31% strand | Q8AAV8 |
| D | Transcriptional regulator arar | protein | 228 | 29% helix, 30% strand | Q8AAV8 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 433 | 0.60 | 0.75 | 52 | empty |
| 2 | 355 | 0.56 | 0.75 | 46 | empty |
| 3 | 153 | 0.55 | 0.81 | 29 | EDO |
| 4 | 157 | 0.52 | 0.80 | 30 | EDO |
| 5 | 150 | 0.52 | 0.79 | 25 | EDO |
Interfaces
3 interfaces between chains.
- C–D · 1662 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1628 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 428 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 35 modified (engineered).
Compared structures
- 5BS6 · Apo structure of transcriptional factor AraR from Bacteroides thetaiotaomicron VPI · 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 Q8AAV8
- Elsewhere: RCSB PDB 5BS6 · PDBe 5BS6 · UniProt Q8AAV8
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