Research workbench
Crystal structure of the streptoccocus suis SEROTYPE2 D- mannonate dehydratase in complex with its substrate
Analyse Crystal structure of the streptoccocus suis SEROTYPE2 D- mannonate dehydratase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DBN
- Type
- protein
- Length
- 698 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mannonate dehydratase
- EC
- 4.2.1.8
- UniProt
- A4VVI4
- Ligands
- CS2, MN
- Pockets
- 6 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mannonate dehydratase (EC 4.2.1.8) | protein | 349 | 38% helix, 15% strand | A4VVI4 |
| B | Mannonate dehydratase (EC 4.2.1.8) | protein | 349 | 37% helix, 16% strand | A4VVI4 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 329 | 0.65 | 0.81 | 45 | CS2 |
| 2 | 258 | 0.62 | 0.81 | 37 | empty |
| 3 | 107 | 0.60 | 0.87 | 22 | empty |
| 4 | 140 | 0.56 | 0.82 | 25 | empty |
| 5 | 53 | 0.50 | 0.87 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 2184 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 3DBN · Crystal structure of the Streptoccocus suis serotype2 D-mannonate dehydratase in complex… · the same entry in another collection · chain A against A, TM-score 1.00
- A4VVI4 · AlphaFold monomer V2.0 prediction for mannonate dehydratase (A4VVI4) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 A4VVI4
- Elsewhere: RCSB PDB 3DBN · PDBe 3DBN · UniProt A4VVI4
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