MolNFT v1 · #92894 · protein
Crystal structure of mannonate dehydratase (target efi-502209) from caulobacter crescentus CB15 complexed with magnesium and D-mannonate
4GME · Mandelate RACEMASE/MUCONATE lactonizing enzyme family: “Crystal structure of mannonate dehydratase (target efi-502209) from caulobacter crescentus CB15 complexed…”. X-ray diffraction, 4 ligands (CS2, MG, CL), 5 pockets (best…
- PDB
- 4GME
- Type
- protein
- Length
- 806 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mandelate RACEMASE/MUCONATE lactonizing enzyme family
- UniProt
- Q9AAR4
- Ligands
- CS2, MG, CL, CO3
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Mandelate RACEMASE/MUCONATE lactonizing enzyme family | protein | 403 | 37% helix, 20% strand | Q9AAR4 |
Ligands and binding sites
- CS2 · D-mannonic acid · ligand · chains A, C
- MG · Magnesium ion · metal · 2 copies · chains A, C
- CL · Chloride ion · ion · 2 copies · chains A, C
- CO3 · Carbonate ion · ion · chains A, C
- GOL · Glycerol · additive · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 431 | 0.82 | 0.90 | 54 | empty |
| 2 | 57 | 0.71 | 0.98 | 22 | CS2 |
| 3 | 53 | 0.71 | 0.98 | 21 | GOL, CO3 |
| 4 | 179 | 0.44 | 0.74 | 28 | empty |
| 5 | 168 | 0.43 | 0.74 | 25 | empty |
Interfaces
1 interface between chains.
- A–C · 2490 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 4GME · Crystal structure of mannonate dehydratase (target EFI-502209) from caulobacter… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9AAR4 · AlphaFold monomer V2.0 prediction for D-mannonate dehydratase CC0532 (Q9AAR4) · a predicted model of the same protein · 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 Q9AAR4
- Elsewhere: RCSB PDB 4GME · PDBe 4GME · UniProt Q9AAR4
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