MolNFT v1 · #157886 · protein
Crystal structure of dtdp-6-deoxy-D-glucose-3,5-epimerase rmlc from legionella pneumophila philadelphia 1 in complex with dtdp-4-keto-L- rhamnose
6NDR · Dtdp-4-dehydrorhamnose 3,5-epimerase: “Crystal structure of dtdp-6-deoxy-D-glucose-3,5-epimerase rmlc from legionella pneumophila philadelphia 1 in…”. X-ray diffraction, 2 ligands (TDO, SO4), 4 pockets (best druggability 0.81).…
- PDB
- 6NDR
- Type
- protein
- Length
- 376 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dtdp-4-dehydrorhamnose 3,5-epimerase
- UniProt
- Q5ZXH5
- Ligands
- TDO, SO4
- Pockets
- 4 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 11% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dtdp-4-dehydrorhamnose 3,5-epimerase | protein | 188 | 11% helix, 45% strand | Q5ZXH5 |
Ligands and binding sites
- TDO · Dtdp-4-keto-L-rhamnose · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 8 copies · 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 | 123 | 0.81 | 0.99 | 28 | EDO |
| 2 | 240 | 0.69 | 0.85 | 26 | TDO |
| 3 | 257 | 0.67 | 0.83 | 33 | TDO |
| 4 | 66 | 0.48 | 0.84 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1717 Ų buried · 43 hydrogen bonds · protein-protein
Compared structures
- 6NDR · Crystal structure of dTDP-6-deoxy-D-glucose-3,5-epimerase RmlC from Legionella… · 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 Q5ZXH5
- Elsewhere: RCSB PDB 6NDR · PDBe 6NDR · UniProt Q5ZXH5
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