MolNFT v1 · #64234 · protein
Crystal structure of rhamnonate dehydratase from gibberella zeae complexed with mg
3FXG: “Crystal structure of rhamnonate dehydratase from gibberella zeae complexed with mg”. X-ray diffraction, 1 ligand (MG), 20 pockets (best druggability 0.83). MolNFT v1 #64234 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 3FXG
- Type
- protein
- Length
- 3,247 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rhamnonate dehydratase
- UniProt
- Q4HYS5
- Ligands
- MG
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Rhamnonate dehydratase | protein | 407 | 39% helix, 15% strand | Q4HYS5 |
| B | Rhamnonate dehydratase | protein | 406 | 39% helix, 15% strand | Q4HYS5 |
| C, D, H | Rhamnonate dehydratase | protein | 405 | 39% helix, 15% strand | Q4HYS5 |
| F, G | Rhamnonate dehydratase | protein | 406 | 39% helix, 16% strand | Q4HYS5 |
Ligands and binding sites
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
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 | 204 | 0.83 | 0.96 | 34 | empty |
| 2 | 178 | 0.83 | 0.97 | 27 | empty |
| 3 | 1006 | 0.82 | 0.83 | 92 | empty |
| 4 | 166 | 0.82 | 0.97 | 23 | empty |
| 5 | 159 | 0.81 | 0.97 | 23 | empty |
Interfaces
16 interfaces between chains.
- G–H · 2653 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 2647 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 2645 Ų buried · 30 hydrogen bonds · protein-protein
- E–F · 2629 Ų buried · 29 hydrogen bonds · protein-protein
- B–E · 1843 Ų buried · 42 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 modified (engineered).
Compared structures
- 3FXG · Crystal structure of rhamnonate dehydratase from Gibberella zeae complexed with Mg · 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
- Every structure of UniProt Q4HYS5
- Elsewhere: RCSB PDB 3FXG · PDBe 3FXG · UniProt Q4HYS5
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