Research workbench
Rmlc P aeruginosa with dtdp-xylose
Analyse Rmlc P aeruginosa with dtdp-xylose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2IXI
- Type
- protein
- Length
- 368 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dtdp-4-dehydrorhamnose 3,5-epimerase
- UniProt
- Q9HU21
- Ligands
- TYD, SRT
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 10% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dtdp-4-dehydrorhamnose 3,5-epimerase | protein | 184 | 10% helix, 46% strand | Q9HU21 |
Ligands and binding sites
- TYD · Thymidine-5'-diphosphate · ligand · 2 copies · chains A, B
- SRT · S,R meso-tartaric acid · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 92 | 0.76 | 0.98 | 23 | empty |
| 2 | 374 | 0.72 | 0.83 | 45 | TYD, SRT |
| 3 | 374 | 0.71 | 0.83 | 46 | TYD |
| 4 | 71 | 0.45 | 0.82 | 33 | empty |
Interfaces
1 interface between chains.
- A–B · 1604 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
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 Q9HU21
- Elsewhere: RCSB PDB 2IXI · PDBe 2IXI · UniProt Q9HU21
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