MolNFT v1 · #73289 · protein
Crystal structure of glucarate dehydratase from burkholderia cepacia complexed with magnesium
3NXL: “Crystal structure of glucarate dehydratase from burkholderia cepacia complexed with magnesium”. X-ray diffraction, 2 ligands (MG, CO3), 8 pockets (best druggability 0.73). MolNFT v1 #73289 on GenesisL1: 3D structure, binding sites…
- PDB
- 3NXL
- Type
- protein
- Length
- 1,697 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucarate dehydratase
- EC
- 4.2.1.40
- UniProt
- Q39KL8
- Ligands
- MG, CO3
- Pockets
- 8 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glucarate dehydratase (EC 4.2.1.40) | protein | 424 | 41% helix, 19% strand | Q39KL8 |
| B | Glucarate dehydratase (EC 4.2.1.40) | protein | 423 | 41% helix, 19% strand | Q39KL8 |
| C, D | Glucarate dehydratase (EC 4.2.1.40) | protein | 425 | 41% helix, 20% strand | Q39KL8 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- CO3 · Carbonate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 389 | 0.73 | 0.84 | 50 | empty |
| 2 | 654 | 0.72 | 0.79 | 70 | CO3 |
| 3 | 207 | 0.69 | 0.87 | 35 | empty |
| 4 | 489 | 0.67 | 0.79 | 51 | CO3 |
| 5 | 449 | 0.66 | 0.79 | 54 | CO3 |
Interfaces
3 interfaces between chains.
- B–D · 1413 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 1388 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 384 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 52 modified (engineered).
Compared structures
- 3NXL · Crystal structure of Glucarate dehydratase from Burkholderia cepacia complexed with… · 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 Q39KL8
- Elsewhere: RCSB PDB 3NXL · PDBe 3NXL · UniProt Q39KL8
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