MolNFT v1 · #136954 · protein
Mutant structures of streptococcus agalactiae gbs glyceraldehyde-3- phosphate dehydrogenase (GAPDH)
5V8Y · Glyceraldehyde-3-phosphate dehydrogenase: “Mutant structures of streptococcus agalactiae gbs glyceraldehyde-3- phosphate dehydrogenase (GAPDH)”. X-ray diffraction, 1 ligand (MG), 6 pockets (best druggability 0.66). MolNFT v1 #136954…
- PDB
- 5V8Y
- Type
- protein
- Length
- 665 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glyceraldehyde-3-phosphate dehydrogenase
- EC
- 1.2.1.-
- UniProt
- Q9ALW2
- Ligands
- MG
- Pockets
- 6 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.-) | protein | 330 | 27% helix, 28% strand | Q9ALW2 |
| B | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.-) | protein | 335 | 27% helix, 30% strand | Q9ALW2 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 662 | 0.66 | 0.76 | 50 | MG |
| 2 | 467 | 0.62 | 0.76 | 56 | empty |
| 3 | 310 | 0.55 | 0.75 | 43 | empty |
| 4 | 94 | 0.37 | 0.75 | 16 | empty |
| 5 | 88 | 0.36 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 613 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5V8Y · Mutant Structures of Streptococcus Agalactiae GBS Glyceraldehyde-3-Phosphate… · 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 Q9ALW2
- Elsewhere: RCSB PDB 5V8Y · PDBe 5V8Y · UniProt Q9ALW2
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