Research workbench
X-ray structures of bacillus pallidus D-arabinose isomerasecomplex with (4R)-2-methylpentane-2,4-diol
Analyse X-ray structures of bacillus pallidus D-arabinose isomerasecomplex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3A9R
- 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
- MN
- Pockets
- 20 · best druggability 0.79
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
- MN · Manganese (II) ion · metal · 6 copies · chains A, B, C
- MRD · (4R)-2-methylpentane-2,4-diol · 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 818 | 0.79 | 0.82 | 86 | empty |
| 2 | 423 | 0.77 | 0.86 | 41 | empty |
| 3 | 423 | 0.76 | 0.85 | 42 | empty |
| 4 | 59 | 0.71 | 0.98 | 18 | MRD, MN |
| 5 | 230 | 0.69 | 0.85 | 38 | empty |
Interfaces
3 interfaces between chains.
- B–C · 2281 Ų buried · 39 hydrogen bonds · protein-protein
- A–C · 2224 Ų buried · 37 hydrogen bonds · protein-protein
- A–B · 2222 Ų buried · 41 hydrogen bonds · protein-protein
Compared structures
- 3A9R · X-ray Structures of Bacillus pallidus D-Arabinose IsomeraseComplex with… · 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 3A9R · PDBe 3A9R · UniProt C0SSE7
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