MolNFT v1 · #125226 · protein
Crystal structure of fumarate hydratase from leishmania major
5L2R: “Crystal structure of fumarate hydratase from leishmania major”. X-ray diffraction, 2 ligands (LMR, SF4), 12 pockets (best druggability 0.84). MolNFT v1 #125226 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5L2R
- Type
- protein
- Length
- 1,063 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fumarate hydratase
- EC
- 4.2.1.2
- UniProt
- E9AE57
- Ligands
- LMR, SF4
- Pockets
- 12 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fumarate hydratase (EC 4.2.1.2) | protein | 532 | 31% helix, 28% strand | E9AE57 |
| B | Fumarate hydratase (EC 4.2.1.2) | protein | 531 | 32% helix, 28% strand | E9AE57 |
Ligands and binding sites
- LMR · (2S)-2-hydroxybutanedioic acid · ligand · 4 copies · chains A, B
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 8 copies · chains A, B
- MLA · Malonic acid · additive · 4 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1060 | 0.84 | 0.85 | 105 | MLA, GOL, PEG |
| 2 | 72 | 0.71 | 0.97 | 30 | LMR, SF4 |
| 3 | 64 | 0.71 | 0.98 | 24 | LMR, SF4 |
| 4 | 209 | 0.48 | 0.75 | 26 | LMR |
| 5 | 196 | 0.46 | 0.75 | 28 | LMR |
Interfaces
1 interface between chains.
- A–B · 4254 Ų buried · 66 hydrogen bonds · protein-protein
Compared structures
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 E9AE57
- Elsewhere: RCSB PDB 5L2R · PDBe 5L2R · UniProt E9AE57
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.