Research workbench
Crystal structure of methanocaldococcus jannaschii fumarate hydratase beta subunit
Analyse Crystal structure of methanocaldococcus jannaschii fumarate hydratase beta… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DNI
- Type
- protein
- Length
- 358 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative L(+)-tartrate dehydratase subunit beta
- EC
- 4.2.1.32
- UniProt
- Q58034
- Ligands
- CL
- Pockets
- 2 · best druggability 0.47
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Putative L(+)-tartrate dehydratase subunit beta (EC 4.2.1.32) | protein | 179 | 27% helix, 36% strand | Q58034 |
Ligands and binding sites
- CL · Chloride ion · ion · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains B, A
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 188 | 0.47 | 0.76 | 26 | empty |
| 2 | 55 | 0.47 | 0.85 | 24 | GOL |
Interfaces
1 interface between chains.
- A–B · 540 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5DNI · Crystal structure of Methanocaldococcus jannaschii Fumarate hydratase beta subunit · the same entry in another collection · chain A against A, TM-score 1.00
- Q58034 · AlphaFold monomer V2.0 prediction for putative L(+)-tartrate dehydratase subunit beta… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q58034
- Elsewhere: RCSB PDB 5DNI · PDBe 5DNI · UniProt Q58034
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