Research workbench
Crystal structure of steptococcus suis mannonate dehydratase with metal mn++
Analyse Crystal structure of steptococcus suis mannonate dehydratase with metal mn++ in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FVM
- 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
- MN
- Pockets
- 8 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mannonate dehydratase (EC 4.2.1.8) | protein | 349 | 38% helix, 17% strand | A4VVI4 |
| B | Mannonate dehydratase (EC 4.2.1.8) | protein | 349 | 37% helix, 16% strand | A4VVI4 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 101 | 0.67 | 0.91 | 22 | empty |
| 2 | 290 | 0.63 | 0.81 | 42 | MN |
| 3 | 268 | 0.63 | 0.81 | 39 | empty |
| 4 | 141 | 0.60 | 0.84 | 25 | empty |
| 5 | 76 | 0.33 | 0.75 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 2178 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 3FVM · Crystal structure of Steptococcus suis mannonate dehydratase with metal Mn++ · 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 3FVM · PDBe 3FVM · UniProt A4VVI4
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