Research workbench
Crystal structure of a fumarate hydratase
Analyse Crystal structure of a fumarate hydratase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HGV
- Type
- protein
- Length
- 1,774 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fumarate hydratase class II
- EC
- 4.2.1.2
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 61% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fumarate hydratase class II (EC 4.2.1.2) | protein | 456 | 62% helix, 8% strand | — |
| B | Fumarate hydratase class II (EC 4.2.1.2) | protein | 453 | 62% helix, 8% strand | — |
| C | Fumarate hydratase class II (EC 4.2.1.2) | protein | 411 | 58% helix, 9% strand | — |
| D | Fumarate hydratase class II (EC 4.2.1.2) | protein | 454 | 60% helix, 8% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 681 | 0.75 | 0.81 | 57 | SO4 |
| 2 | 788 | 0.74 | 0.79 | 63 | SO4 |
| 3 | 528 | 0.65 | 0.77 | 57 | empty |
| 4 | 361 | 0.62 | 0.78 | 33 | empty |
| 5 | 347 | 0.62 | 0.78 | 46 | SO4 |
Interfaces
6 interfaces between chains.
- A–B · 3025 Ų buried · 33 hydrogen bonds · protein-protein
- C–D · 2959 Ų buried · 32 hydrogen bonds · protein-protein
- A–D · 2532 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 2498 Ų buried · 27 hydrogen bonds · protein-protein
- B–D · 1911 Ų buried · 46 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 42 modified (engineered).
Compared structures
- 4HGV · Crystal structure of a fumarate hydratase · the same entry in another collection · 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
- Elsewhere: RCSB PDB 4HGV · PDBe 4HGV
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