MolNFT v1 · #157233 · protein
Crystal structure of cytosolic fumarate hydratase from leishmania major in a complex with inhibitor thiomalate
6MSN: “Crystal structure of cytosolic fumarate hydratase from leishmania major in a complex with inhibitor thiomalate”. X-ray diffraction, 2 ligands (SF4, JYD), 12 pockets (best druggability 0.83). MolNFT v1 #157233 on GenesisL1: 3D…
- PDB
- 6MSN
- 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
- SF4, JYD
- Pockets
- 12 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fumarate hydratase (EC 4.2.1.2) | protein | 532 | 32% helix, 29% strand | E9AE57 |
| B | Fumarate hydratase (EC 4.2.1.2) | protein | 531 | 32% helix, 29% strand | E9AE57 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains A, B
- JYD · (2S)-2-sulfanylbutanedioic acid · ligand · 2 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1126 | 0.83 | 0.84 | 112 | empty |
| 2 | 66 | 0.72 | 0.98 | 25 | SF4, JYD |
| 3 | 77 | 0.72 | 0.97 | 29 | SF4, JYD |
| 4 | 199 | 0.48 | 0.76 | 20 | empty |
| 5 | 218 | 0.46 | 0.74 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 4185 Ų buried · 63 hydrogen bonds · protein-protein
Compared structures
- 6MSN · Crystal structure of cytosolic fumarate hydratase from Leishmania major in a complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- E9AE57 · AlphaFold monomer V2.0 prediction for fumarate hydratase 2 (E9AE57) · 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 E9AE57
- Elsewhere: RCSB PDB 6MSN · PDBe 6MSN · UniProt E9AE57
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