Research workbench
Crystal structure of fusobacterium nucleatum tannase
Analyse Crystal structure of fusobacterium nucleatum tannase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YQ4
- Type
- protein
- Length
- 1,436 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tannase
- UniProt
- Q8RFS1
- Ligands
- SPD, MG
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tannase | protein | 478 | 35% helix, 18% strand | Q8RFS1 |
| B | Tannase | protein | 480 | 36% helix, 17% strand | Q8RFS1 |
| C | Tannase | protein | 478 | 35% helix, 17% strand | Q8RFS1 |
Ligands and binding sites
- SPD · Spermidine · ligand · chains B
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
- GOL · Glycerol · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 736 | 0.74 | 0.79 | 63 | GOL |
| 2 | 502 | 0.73 | 0.82 | 59 | empty |
| 3 | 767 | 0.72 | 0.78 | 72 | empty |
| 4 | 369 | 0.65 | 0.80 | 37 | empty |
| 5 | 225 | 0.65 | 0.84 | 32 | GOL, SPD |
Interfaces
3 interfaces between chains.
- A–B · 768 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 474 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 264 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6YQ4 · Crystal structure of Fusobacterium nucleatum tannase · 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 Q8RFS1
- Elsewhere: RCSB PDB 6YQ4 · PDBe 6YQ4 · UniProt Q8RFS1
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