Research workbench
Crystal structure of mannonate dehydratase from escherichia COLI strain K12
Analyse Crystal structure 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
- 4EAC
- 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
- MN, CL
- Pockets
- 10 · best druggability 0.77
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 | 45% helix, 13% strand | P24215 |
| C | Mannonate dehydratase (EC 4.2.1.8) | protein | 396 | 46% helix, 13% strand | P24215 |
Ligands and binding sites
- 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
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 112 | 0.77 | 0.97 | 40 | empty |
| 2 | 99 | 0.77 | 0.98 | 33 | empty |
| 3 | 155 | 0.54 | 0.81 | 27 | empty |
| 4 | 186 | 0.48 | 0.76 | 25 | empty |
| 5 | 119 | 0.41 | 0.76 | 31 | empty |
Interfaces
3 interfaces between chains.
- A–B · 331 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 305 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 14 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4EAC · Crystal structure of mannonate dehydratase from Escherichia coli strain K12 · 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 4EAC · PDBe 4EAC · UniProt P24215
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