MolNFT v1 · #149966 · protein
Cyanobacterial GAPDH with NAD and CP12 bound
6GFQ · Glyceraldehyde-3-phosphate dehydrogenase: “Cyanobacterial GAPDH with NAD and CP12 bound”. X-ray diffraction, 2 ligands (NAD, MG), 4 pockets (best druggability 0.74). MolNFT v1 #149966 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6GFQ
- Type
- protein
- Length
- 698 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glyceraldehyde-3-phosphate dehydrogenase; CP12 polypeptide
- EC
- 1.2.1.-
- UniProt
- Q8DIW5, Q8DHX3
- Ligands
- NAD, MG
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.-) | protein | 338 | 31% helix, 28% strand | Q8DIW5 |
| C | CP12 polypeptide | protein | 22 | 36% helix, 0% strand | Q8DHX3 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B, C
- 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
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 583 | 0.74 | 0.81 | 72 | NAD |
| 2 | 356 | 0.62 | 0.78 | 43 | NAD |
| 3 | 403 | 0.58 | 0.75 | 44 | empty |
| 4 | 56 | 0.33 | 0.78 | 15 | NAD |
Interfaces
2 interfaces between chains.
- B–C · 807 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 516 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6GFQ · cyanobacterial GAPDH with NAD and CP12 bound · 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 Q8DIW5
- Every structure of UniProt Q8DHX3
- Elsewhere: RCSB PDB 6GFQ · PDBe 6GFQ · UniProt Q8DIW5 · UniProt Q8DHX3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.