MolNFT v1 · #81578 · protein
Crystal structure of L-rhamnose isomerase mutant W38F from bacillus halodurans in complex with mn
3UVA: “Crystal structure of L-rhamnose isomerase mutant W38F from bacillus halodurans in complex with mn”. X-ray diffraction, 1 ligand (MN), 20 pockets (best druggability 0.62). MolNFT v1 #81578 on GenesisL1: 3D structure, binding sites…
- PDB
- 3UVA
- Type
- protein
- Length
- 1,614 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 0.62
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-rhamnose isomerase (EC 5.3.1.14) | protein | 402 | 47% helix, 12% strand | Q9KCL9 |
| B | L-rhamnose isomerase (EC 5.3.1.14) | protein | 404 | 48% helix, 12% strand | Q9KCL9 |
| C | L-rhamnose isomerase (EC 5.3.1.14) | protein | 405 | 49% helix, 12% strand | Q9KCL9 |
| D | L-rhamnose isomerase (EC 5.3.1.14) | protein | 403 | 49% helix, 12% 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 315 | 0.62 | 0.79 | 45 | empty |
| 2 | 312 | 0.62 | 0.79 | 48 | MN |
| 3 | 292 | 0.62 | 0.79 | 41 | MN |
| 4 | 305 | 0.62 | 0.79 | 36 | MN |
| 5 | 254 | 0.59 | 0.79 | 52 | empty |
Interfaces
3 interfaces between chains.
- A–C · 2557 Ų buried · 35 hydrogen bonds · protein-protein
- B–D · 2508 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 304 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3UVA · Crystal structure of L-rhamnose isomerase mutant W38F from Bacillus halodurans in complex… · 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 C 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 3UVA · PDBe 3UVA · UniProt Q9KCL9
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