Research workbench
Differential regulation of the xylan degrading apparatus of cellvibrio japonicus by a novel two component system
Analyse Differential regulation of the xylan degrading apparatus of cellvibrio… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VA0
- Type
- protein
- Length
- 634 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Abfs arabinofuranosidase two component system sensor protein
- UniProt
- B3PFT7
- Ligands
- PO4, CL
- Pockets
- 5 · best druggability 0.62
Structure
x-ray diffraction · 5 distinct chains · 36% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | Abfs arabinofuranosidase two component system sensor protein | protein | 99 | 33% helix, 25% strand | B3PFT7 |
| B | Abfs arabinofuranosidase two component system sensor protein | protein | 119 | 39% helix, 23% strand | B3PFT7 |
| C | Abfs arabinofuranosidase two component system sensor protein | protein | 99 | 33% helix, 27% strand | B3PFT7 |
| D | Abfs arabinofuranosidase two component system sensor protein | protein | 98 | 34% helix, 28% strand | B3PFT7 |
| E | Abfs arabinofuranosidase two component system sensor protein | protein | 120 | 41% helix, 23% strand | B3PFT7 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 6 copies · chains A, B, C, D, E, F
- CL · Chloride ion · ion · 3 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 338 | 0.62 | 0.78 | 41 | empty |
| 2 | 297 | 0.62 | 0.79 | 33 | empty |
| 3 | 58 | 0.40 | 0.81 | 23 | CL |
| 4 | 92 | 0.37 | 0.76 | 21 | empty |
| 5 | 52 | 0.28 | 0.74 | 14 | empty |
Interfaces
9 interfaces between chains.
- A–B · 612 Ų buried · 9 hydrogen bonds · protein-protein
- E–F · 608 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 591 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 350 Ų buried · 8 hydrogen bonds · protein-protein
- D–E · 348 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 2VA0 · Differential regulation of the xylan degrading apparatus of Cellvibrio japonicus by a… · 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 B3PFT7
- Elsewhere: RCSB PDB 2VA0 · PDBe 2VA0 · UniProt B3PFT7
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