MolNFT v1 · #136953 · protein
Mutant structures of streptococcus agalactiae gbs glyceraldehyde-3- phosphate dehydrogenase (GAPDH)
5V8X · Glyceraldehyde-3-phosphate dehydrogenase: “Mutant structures of streptococcus agalactiae gbs glyceraldehyde-3- phosphate dehydrogenase (GAPDH)”. X-ray diffraction, 2 ligands (NAD, MG), 17 pockets (best druggability 0.81). MolNFT v1…
- PDB
- 5V8X
- Type
- protein
- Length
- 1,316 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glyceraldehyde-3-phosphate dehydrogenase
- EC
- 1.2.1.-
- UniProt
- Q9ALW2
- Ligands
- NAD, MG
- Pockets
- 17 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 29% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.-) | protein | 334 | 29% helix, 28% strand | Q9ALW2 |
| B | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.-) | protein | 334 | 29% helix, 29% strand | Q9ALW2 |
| C | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.-) | protein | 329 | 29% helix, 28% strand | Q9ALW2 |
| D | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.-) | protein | 319 | 30% helix, 27% strand | Q9ALW2 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, C, B, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1151 | 0.81 | 0.82 | 107 | empty |
| 2 | 1066 | 0.80 | 0.81 | 111 | NAD |
| 3 | 1103 | 0.80 | 0.81 | 103 | NAD |
| 4 | 212 | 0.64 | 0.83 | 34 | empty |
| 5 | 65 | 0.40 | 0.80 | 19 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2034 Ų buried · 40 hydrogen bonds · protein-protein
- C–D · 2028 Ų buried · 50 hydrogen bonds · protein-protein
- A–C · 1392 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 1390 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 578 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5V8X · 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 5V8X · PDBe 5V8X · UniProt Q9ALW2
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