MolNFT v1 · #105187 · protein
Crystal structure of glyceraldehyde-3-phosphate dehydrogenase from streptococcus agalactiae NEM316 at 2.46 ångström resolution
4QX6 · Glyceraldehyde 3-phosphate dehydrogenase: “Crystal structure of glyceraldehyde-3-phosphate dehydrogenase from streptococcus agalactiae NEM316 at 2.46…”. X-ray diffraction, 1 ligand (NAD), 15 pockets (best druggability 0.81). MolNFT…
- PDB
- 4QX6
- Type
- protein
- Length
- 1,345 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glyceraldehyde 3-phosphate dehydrogenase
- EC
- 1.2.1.12
- UniProt
- Q8E3E8
- Ligands
- NAD
- Pockets
- 15 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 28% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glyceraldehyde 3-phosphate dehydrogenase (EC 1.2.1.12) | protein | 332 | 28% helix, 29% strand | Q8E3E8 |
| B | Glyceraldehyde 3-phosphate dehydrogenase (EC 1.2.1.12) | protein | 335 | 28% helix, 29% strand | Q8E3E8 |
| C | Glyceraldehyde 3-phosphate dehydrogenase (EC 1.2.1.12) | protein | 334 | 28% helix, 29% strand | Q8E3E8 |
| D | Glyceraldehyde 3-phosphate dehydrogenase (EC 1.2.1.12) | protein | 344 | 27% helix, 28% strand | Q8E3E8 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1063 | 0.81 | 0.82 | 108 | empty |
| 2 | 1038 | 0.80 | 0.81 | 120 | NAD |
| 3 | 1028 | 0.80 | 0.81 | 109 | NAD, EDO |
| 4 | 96 | 0.40 | 0.77 | 22 | empty |
| 5 | 82 | 0.37 | 0.77 | 17 | empty |
Interfaces
6 interfaces between chains.
- B–D · 2044 Ų buried · 48 hydrogen bonds · protein-protein
- A–C · 2019 Ų buried · 43 hydrogen bonds · protein-protein
- A–B · 1388 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1384 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 588 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 4QX6 · CRYSTAL STRUCTURE OF GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE FROM STREPTOCOCCUS… · 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 Q8E3E8
- Elsewhere: RCSB PDB 4QX6 · PDBe 4QX6 · UniProt Q8E3E8
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