Research workbench
Crystal structure of evaa, a 2,3-dehydratase in complex with dtdp- benzene and dtdp-rhamnose
Analyse Crystal structure of evaa, a 2,3-dehydratase in complex with dtdp- benzene and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4J7H
- Type
- protein
- Length
- 890 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Evaa 2,3-dehydratase
- UniProt
- O52793
- Ligands
- TLO, TRH
- Pockets
- 12 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 23% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Evaa 2,3-dehydratase | protein | 446 | 23% helix, 35% strand | O52793 |
| B | Evaa 2,3-dehydratase | protein | 444 | 23% helix, 36% strand | O52793 |
Ligands and binding sites
- TLO · 5'-O-[(S)-hydroxy{[(s)-hydroxy(phenoxy) phosphoryl]oxy}phosphoryl]thymidine · ligand · 2 copies · chains A, B
- TRH · 2'-deoxy-thymidine-beta-L-rhamnose · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 606 | 0.74 | 0.81 | 58 | TRH |
| 2 | 614 | 0.73 | 0.80 | 59 | TRH |
| 3 | 434 | 0.72 | 0.82 | 57 | TLO |
| 4 | 432 | 0.68 | 0.80 | 49 | TLO |
| 5 | 305 | 0.58 | 0.77 | 34 | EDO |
Interfaces
1 interface between chains.
- A–B · 363 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4J7H · Crystal structure of EvaA, a 2,3-dehydratase in complex with dTDP-benzene and… · the same entry in another collection · chain A against A, TM-score 1.00
- O52793 · AlphaFold monomer V2.0 prediction for dtdp-4-dehydro-6-deoxy-alpha-D- glucopyranose… · a predicted model of the same protein · chain B 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 O52793
- Elsewhere: RCSB PDB 4J7H · PDBe 4J7H · UniProt O52793
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