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1.63 ångström resolution crystal structure of dtdp-4-dehydrorhamnose 3,5-epimerase (rfbc) from bacillus anthracis str. ames with tdp and ppi bound
Analyse 1.63 ångström resolution crystal structure of dtdp-4-dehydrorhamnose… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RYK
- Type
- protein
- Length
- 350 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dtdp-4-dehydrorhamnose 3,5-epimerase
- EC
- 5.1.3.13
- UniProt
- Q81TP1
- Ligands
- POP, TYD
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 6% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dtdp-4-dehydrorhamnose 3,5-epimerase (EC 5.1.3.13) | protein | 175 | 6% helix, 47% strand | Q81TP1 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 340 | 0.69 | 0.83 | 39 | POP |
| 2 | 348 | 0.68 | 0.81 | 34 | TYD |
| 3 | 82 | 0.58 | 0.87 | 20 | empty |
| 4 | 55 | 0.47 | 0.85 | 17 | empty |
| 5 | 51 | 0.34 | 0.78 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1519 Ų buried · 34 hydrogen bonds · protein-protein
Compared structures
- 3RYK · 1.63 Angstrom resolution crystal structure of dTDP-4-dehydrorhamnose 3,5-epimerase (rfbC)… · 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 Q81TP1
- Elsewhere: RCSB PDB 3RYK · PDBe 3RYK · UniProt Q81TP1
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