Research workbench
Crystal structure of L-rhamnose isomerase W38A mutant from bacillus halodurans
Analyse Crystal structure of L-rhamnose isomerase W38A mutant from bacillus halodurans in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3UXI
- Type
- protein
- Length
- 1,612 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-rhamnose isomerase
- EC
- 5.3.1.14
- UniProt
- Q9KCL9
- Ligands
- MN
- Pockets
- 16 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | L-rhamnose isomerase (EC 5.3.1.14) | protein | 402 | 47% helix, 12% strand | Q9KCL9 |
| C, D | L-rhamnose isomerase (EC 5.3.1.14) | protein | 404 | 49% helix, 12% strand | Q9KCL9 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 993 | 0.88 | 0.90 | 165 | empty |
| 2 | 257 | 0.77 | 0.90 | 43 | empty |
| 3 | 1033 | 0.77 | 0.79 | 126 | MN |
| 4 | 1112 | 0.75 | 0.78 | 124 | empty |
| 5 | 327 | 0.74 | 0.86 | 51 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2578 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 2552 Ų buried · 35 hydrogen bonds · protein-protein
- A–C · 1983 Ų buried · 29 hydrogen bonds · protein-protein
- B–D · 1900 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 904 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 3UXI · Crystal structure of L-rhamnose isomerase W38A mutant from Bacillus halodurans · the same entry in another collection · chain A against A, TM-score 1.00
- Q9KCL9 · AlphaFold monomer V2.0 prediction for L-rhamnose isomerase (Q9KCL9) · a predicted model of the same protein · 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 Q9KCL9
- Elsewhere: RCSB PDB 3UXI · PDBe 3UXI · UniProt Q9KCL9
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