Research workbench
Crystal structures of mannonate dehydratase from escherichia COLI strain K12 complexed with D-mannonate
Analyse Crystal structures of mannonate dehydratase from escherichia COLI strain K12… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4EAY
- Type
- protein
- Length
- 1,581 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mannonate dehydratase
- EC
- 4.2.1.8
- UniProt
- P24215
- Ligands
- CS2, MN, CL
- Pockets
- 13 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Mannonate dehydratase (EC 4.2.1.8) | protein | 395 | 46% helix, 13% strand | P24215 |
| C | Mannonate dehydratase (EC 4.2.1.8) | protein | 396 | 45% helix, 13% strand | P24215 |
Ligands and binding sites
- CS2 · D-mannonic acid · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
- CL · Chloride 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
13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 108 | 0.78 | 0.98 | 41 | empty |
| 2 | 92 | 0.76 | 0.98 | 33 | empty |
| 3 | 160 | 0.56 | 0.81 | 29 | empty |
| 4 | 194 | 0.49 | 0.76 | 24 | empty |
| 5 | 83 | 0.40 | 0.78 | 19 | empty |
Interfaces
2 interfaces between chains.
- A–B · 338 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 329 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4EAY · Crystal structures of mannonate dehydratase from Escherichia coli strain K12 complexed… · the same entry in another collection · chain A against A, TM-score 1.00
- P24215 · AlphaFold monomer V2.0 prediction for mannonate dehydratase (P24215) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 P24215
- Elsewhere: RCSB PDB 4EAY · PDBe 4EAY · UniProt P24215
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.