Research workbench
Crystal structure of L-rhamnose isomerase from bacillus halodurans in complex with mn
Analyse Crystal structure of L-rhamnose isomerase from bacillus halodurans in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3UU0
- Type
- protein
- Length
- 1,610 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
- 20 · best druggability 0.67
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-rhamnose isomerase (EC 5.3.1.14) | protein | 401 | 49% helix, 11% strand | Q9KCL9 |
| B | L-rhamnose isomerase (EC 5.3.1.14) | protein | 402 | 49% helix, 12% strand | Q9KCL9 |
| C | L-rhamnose isomerase (EC 5.3.1.14) | protein | 403 | 48% helix, 12% strand | Q9KCL9 |
| D | L-rhamnose isomerase (EC 5.3.1.14) | protein | 404 | 47% helix, 11% strand | Q9KCL9 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 373 | 0.67 | 0.80 | 60 | empty |
| 2 | 351 | 0.64 | 0.79 | 58 | empty |
| 3 | 308 | 0.62 | 0.79 | 51 | empty |
| 4 | 316 | 0.62 | 0.79 | 40 | empty |
| 5 | 259 | 0.61 | 0.80 | 34 | MN |
Interfaces
3 interfaces between chains.
- A–C · 2561 Ų buried · 32 hydrogen bonds · protein-protein
- B–D · 2502 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 299 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3UU0 · Crystal structure of L-rhamnose isomerase from Bacillus halodurans in complex with Mn · the same entry in another collection · chain D against D, 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 3UU0 · PDBe 3UU0 · UniProt Q9KCL9
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