Research workbench
Cyanobacterial GAPDH with NADP bound
Analyse Cyanobacterial GAPDH with NADP bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GFP
- Type
- protein
- Length
- 676 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
- Q8DIW5
- Ligands
- NAP, NAD, MG
- Pockets
- 5 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.-) | protein | 338 | 32% helix, 28% strand | Q8DIW5 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains B
- MLI · Malonate ion · additive · 2 copies · chains A, B
- FMT · Formic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 347 | 0.64 | 0.80 | 36 | NAP, NAD, MLI |
| 2 | 337 | 0.63 | 0.79 | 35 | NAP, NAD, MLI, FMT |
| 3 | 344 | 0.54 | 0.74 | 45 | empty |
| 4 | 181 | 0.48 | 0.76 | 27 | empty |
| 5 | 53 | 0.31 | 0.77 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 534 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6GFP · cyanobacterial GAPDH with NADP 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
- Elsewhere: RCSB PDB 6GFP · PDBe 6GFP · UniProt Q8DIW5
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