Research workbench
X-ray structure of bacillus pallidus D-arabinose isomerase complex with L-fucitol
Analyse X-ray structure of bacillus pallidus D-arabinose isomerase complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3A9T
- Type
- protein
- Length
- 1,767 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-arabinose isomerase
- EC
- 5.3.1.3
- UniProt
- C0SSE7
- Ligands
- FOC, MN
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | D-arabinose isomerase (EC 5.3.1.3) | protein | 589 | 41% helix, 20% strand | C0SSE7 |
Ligands and binding sites
- FOC · Fucitol · ligand · 3 copies · chains A, B, C
- MN · Manganese (II) ion · metal · 6 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, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 414 | 0.78 | 0.87 | 42 | empty |
| 2 | 650 | 0.76 | 0.82 | 69 | empty |
| 3 | 391 | 0.73 | 0.84 | 37 | empty |
| 4 | 53 | 0.71 | 0.98 | 18 | FOC, MN |
| 5 | 50 | 0.70 | 0.98 | 15 | FOC, MN |
Interfaces
3 interfaces between chains.
- B–C · 2282 Ų buried · 40 hydrogen bonds · protein-protein
- A–C · 2242 Ų buried · 41 hydrogen bonds · protein-protein
- A–B · 2217 Ų buried · 39 hydrogen bonds · protein-protein
Compared structures
- 3A9T · X-ray Structure of Bacillus pallidus D-Arabinose Isomerase Complex with L-Fucitol · 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 C0SSE7
- Elsewhere: RCSB PDB 3A9T · PDBe 3A9T · UniProt C0SSE7
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