Research workbench
Crystal structure of dtdp-4-dehydrorhamnose 3,5-epimerase from sulfolobus tokodaii
Analyse Crystal structure of dtdp-4-dehydrorhamnose 3,5-epimerase from sulfolobus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2B9U
- Type
- protein
- Length
- 2,112 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical dtdp-4-dehydrorhamnose 3,5-epimerase
- EC
- 5.1.3.13
- UniProt
- Q96Z62
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 9% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, B, E, F, G, H, I, J, K, L | Hypothetical dtdp-4-dehydrorhamnose 3,5-epimerase (EC 5.1.3.13) | protein | 176 | 9% helix, 51% strand | Q96Z62 |
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 907 | 0.83 | 0.85 | 99 | empty |
| 2 | 852 | 0.79 | 0.82 | 85 | empty |
| 3 | 333 | 0.75 | 0.86 | 27 | empty |
| 4 | 239 | 0.75 | 0.89 | 28 | empty |
| 5 | 630 | 0.75 | 0.81 | 51 | empty |
Interfaces
29 interfaces between chains.
- K–L · 1808 Ų buried · 35 hydrogen bonds · protein-protein
- I–J · 1800 Ų buried · 37 hydrogen bonds · protein-protein
- A–C · 1790 Ų buried · 32 hydrogen bonds · protein-protein
- E–F · 1784 Ų buried · 36 hydrogen bonds · protein-protein
- D–B · 1742 Ų buried · 37 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 2B9U · Crystal structure of dTDP-4-dehydrorhamnose 3,5-epimerase from sulfolobus tokodaii · 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 Q96Z62
- Elsewhere: RCSB PDB 2B9U · PDBe 2B9U · UniProt Q96Z62
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