Research workbench
Crystal structure of dtdp-4-dehydrorhamnose 3,5-epimerase from elizabethkingia anophelis NUHP1
Analyse Crystal structure of dtdp-4-dehydrorhamnose 3,5-epimerase from elizabethkingia… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6C46
- Type
- protein
- Length
- 914 residues
- Chains
- 5
- 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
- A0A077ENB9
- Ligands
- CA
- Pockets
- 16 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 12% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E | Dtdp-4-dehydrorhamnose 3,5-epimerase (EC 5.1.3.13) | protein | 183 | 13% helix, 44% strand | A0A077ENB9 |
| C | Dtdp-4-dehydrorhamnose 3,5-epimerase (EC 5.1.3.13) | protein | 182 | 12% helix, 43% strand | A0A077ENB9 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 83 | 0.73 | 0.96 | 23 | empty |
| 2 | 77 | 0.72 | 0.96 | 25 | empty |
| 3 | 418 | 0.67 | 0.80 | 45 | empty |
| 4 | 413 | 0.67 | 0.80 | 43 | empty |
| 5 | 411 | 0.65 | 0.79 | 52 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1242 Ų buried · 32 hydrogen bonds · protein-protein
- C–D · 1164 Ų buried · 30 hydrogen bonds · protein-protein
- D–E · 603 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 552 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6C46 · Crystal structure of dTDP-4-dehydrorhamnose 3,5-epimerase from Elizabethkingia anophelis… · 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 A0A077ENB9
- Elsewhere: RCSB PDB 6C46 · PDBe 6C46 · UniProt A0A077ENB9
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