Research workbench
Crystal structure of mitochondrial fumarate hydratase from leishmania major in a complex with inhibitor thiomalate
Analyse Crystal structure of mitochondrial fumarate hydratase from leishmania major in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MSO
- Type
- protein
- Length
- 2,139 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fumarate hydratase
- EC
- 4.2.1.2
- UniProt
- Q4QAU9
- Ligands
- SF4, JYD
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Fumarate hydratase (EC 4.2.1.2) | protein | 540 | 32% helix, 27% strand | Q4QAU9 |
| C | Fumarate hydratase (EC 4.2.1.2) | protein | 528 | 31% helix, 29% strand | Q4QAU9 |
| D | Fumarate hydratase (EC 4.2.1.2) | protein | 531 | 30% helix, 27% strand | Q4QAU9 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 4 copies · chains A, B, C, D
- JYD · (2S)-2-sulfanylbutanedioic acid · ligand · 4 copies · chains A, B, C, D
- 1PE · Pentaethylene glycol · additive · 10 copies · chains A, B, C, D
- GOL · Glycerol · additive · 8 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 100 | 0.76 | 0.96 | 28 | empty |
| 2 | 102 | 0.75 | 0.95 | 29 | empty |
| 3 | 75 | 0.72 | 0.97 | 25 | SF4, JYD |
| 4 | 75 | 0.72 | 0.97 | 25 | SF4, JYD |
| 5 | 74 | 0.72 | 0.97 | 25 | SF4, JYD |
Interfaces
3 interfaces between chains.
- A–B · 4596 Ų buried · 63 hydrogen bonds · protein-protein
- C–D · 4352 Ų buried · 60 hydrogen bonds · protein-protein
- A–C · 409 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6MSO · Crystal structure of mitochondrial fumarate hydratase from Leishmania major in a complex… · the same entry in another collection · chain D against D, TM-score 1.00
- Q4QAU9 · AlphaFold monomer V2.0 prediction for fumarate hydratase 1, mitochondrial (Q4QAU9) · a predicted model of the same protein · 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 Q4QAU9
- Elsewhere: RCSB PDB 6MSO · PDBe 6MSO · UniProt Q4QAU9
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