Research workbench
Crystal structure of cytosolic fumarate hydratase from leishmania major
Analyse Crystal structure of cytosolic fumarate hydratase from leishmania major in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6UNZ
- Type
- protein
- Length
- 4,260 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fumarate hydratase 2
- EC
- 4.2.1.2
- UniProt
- E9AE57
- Ligands
- SF4
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 6 distinct chains · 31% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fumarate hydratase 2 (EC 4.2.1.2) | protein | 539 | 31% helix, 25% strand | E9AE57 |
| B | Fumarate hydratase 2 (EC 4.2.1.2) | protein | 534 | 32% helix, 26% strand | E9AE57 |
| C, G | Fumarate hydratase 2 (EC 4.2.1.2) | protein | 532 | 31% helix, 28% strand | E9AE57 |
| D | Fumarate hydratase 2 (EC 4.2.1.2) | protein | 530 | 31% helix, 28% strand | E9AE57 |
| E | Fumarate hydratase 2 (EC 4.2.1.2) | protein | 531 | 31% helix, 27% strand | E9AE57 |
| F, H | Fumarate hydratase 2 (EC 4.2.1.2) | protein | 531 | 31% helix, 29% strand | E9AE57 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- GOL · Glycerol · additive · 2 copies · chains A, B, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1133 | 0.86 | 0.87 | 148 | empty |
| 2 | 901 | 0.85 | 0.87 | 100 | empty |
| 3 | 1008 | 0.84 | 0.85 | 105 | empty |
| 4 | 963 | 0.83 | 0.84 | 93 | empty |
| 5 | 577 | 0.82 | 0.87 | 71 | empty |
Interfaces
9 interfaces between chains.
- E–F · 4245 Ų buried · 62 hydrogen bonds · protein-protein
- A–B · 4179 Ų buried · 52 hydrogen bonds · protein-protein
- G–H · 4160 Ų buried · 68 hydrogen bonds · protein-protein
- C–D · 3824 Ų buried · 47 hydrogen bonds · protein-protein
- B–F · 264 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6UNZ · Crystal structure of cytosolic fumarate hydratase from Leishmania major · the same entry in another collection · chain H against H, TM-score 1.00
- E9AE57 · AlphaFold monomer V2.0 prediction for fumarate hydratase 2 (E9AE57) · a predicted model of the same protein · chain F 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 E9AE57
- Elsewhere: RCSB PDB 6UNZ · PDBe 6UNZ · UniProt E9AE57
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