MolNFT v1 · #53470 · protein
H309A mutant of mannosyl-3-phosphoglycerate synthase from thermus thermophilus HB27 in complex with GDP-alpha-D-mannose and MG(II)
2WVM: “H309A mutant of mannosyl-3-phosphoglycerate synthase from thermus thermophilus HB27 in complex with…”. X-ray diffraction, 3 ligands (GDD, ZN, MG), 5 pockets (best druggability 0.74). MolNFT v1 #53470 on GenesisL1: 3D structure…
- PDB
- 2WVM
- Type
- protein
- Length
- 747 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mannosyl-3-phosphoglycerate synthase
- EC
- 2.4.1.217
- UniProt
- Q72K30
- Ligands
- GDD, ZN, MG
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mannosyl-3-phosphoglycerate synthase (EC 2.4.1.217) | protein | 375 | 44% helix, 18% strand | Q72K30 |
| B | Mannosyl-3-phosphoglycerate synthase (EC 2.4.1.217) | protein | 372 | 43% helix, 19% strand | Q72K30 |
Ligands and binding sites
- GDD · Guanosine-5'-diphosphate-alpha-D-mannose · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 3 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 768 | 0.74 | 0.79 | 59 | GDD, MG |
| 2 | 662 | 0.70 | 0.78 | 49 | GDD, MG |
| 3 | 150 | 0.45 | 0.76 | 21 | empty |
| 4 | 108 | 0.40 | 0.76 | 18 | empty |
| 5 | 89 | 0.33 | 0.74 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1700 Ų buried · 38 hydrogen bonds · protein-protein
Compared structures
- 2WVM · H309A mutant of Mannosyl-3-phosphoglycerate synthase from Thermus thermophilus HB27 in… · the same entry in another collection · 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 Q72K30
- Elsewhere: RCSB PDB 2WVM · PDBe 2WVM · UniProt Q72K30
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