MolNFT v1 · #165725 · protein
Crystal structure of recombinant class II fumarase from schistosoma mansoni
6U4O · Fumarate hydratase: “Crystal structure of recombinant class II fumarase from schistosoma mansoni”. X-ray diffraction, 1 ligand (LMR), 18 pockets (best druggability 0.77). MolNFT v1 #165725 on GenesisL1: 3D structure, binding sites…
- PDB
- 6U4O
- Type
- protein
- Length
- 1,912 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fumarate hydratase
- EC
- 4.2.1.2
- Ligands
- LMR
- Pockets
- 18 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 61% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Fumarate hydratase (EC 4.2.1.2) | protein | 477 | 61% helix, 7% strand | — |
| A | Fumarate hydratase (EC 4.2.1.2) | protein | 479 | 61% helix, 8% strand | — |
| D | Fumarate hydratase (EC 4.2.1.2) | protein | 478 | 61% helix, 8% strand | — |
| B | Fumarate hydratase (EC 4.2.1.2) | protein | 478 | 62% helix, 7% strand | — |
Ligands and binding sites
- LMR · (2S)-2-hydroxybutanedioic acid · ligand · 4 copies · chains C, A, D, B
- GOL · Glycerol · additive · 4 copies · chains C, D, A, B
- ACT · Acetate ion · additive · 4 copies · chains C, A, D, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 811 | 0.77 | 0.81 | 66 | GOL |
| 2 | 737 | 0.76 | 0.81 | 67 | GOL |
| 3 | 363 | 0.64 | 0.79 | 46 | GOL |
| 4 | 379 | 0.64 | 0.79 | 49 | GOL |
| 5 | 352 | 0.62 | 0.78 | 42 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2938 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 2910 Ų buried · 30 hydrogen bonds · protein-protein
- A–D · 111 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6U4O · Crystal structure of recombinant class II fumarase from Schistosoma mansoni · the same entry in another collection · chain C against C, 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 6U4O · PDBe 6U4O
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