MolNFT v1 · #179142 · protein
Crystal structure of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from mycoplasma genitalium with bound NAD
7JWK: “Crystal structure of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from mycoplasma genitalium with bound…”. X-ray diffraction, 2 ligands (NAD, PO4), 14 pockets (best druggability 0.82). MolNFT v1 #179142 on GenesisL1: 3D…
- PDB
- 7JWK
- Type
- protein
- Length
- 1,323 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
- P47543
- Ligands
- NAD, PO4
- Pockets
- 14 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 29% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) | protein | 331 | 28% helix, 29% strand | P47543 |
| C | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) | protein | 333 | 29% helix, 29% strand | P47543 |
| D | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) | protein | 328 | 29% helix, 30% strand | P47543 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, C, B, D
- PO4 · Phosphate ion · ion · 8 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1184 | 0.82 | 0.83 | 127 | PEG |
| 2 | 1134 | 0.78 | 0.80 | 104 | NAD, PO4 |
| 3 | 591 | 0.74 | 0.81 | 61 | NAD, PO4 |
| 4 | 414 | 0.68 | 0.80 | 47 | NAD, PO4 |
| 5 | 69 | 0.36 | 0.77 | 9 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1937 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 1920 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 1383 Ų buried · 21 hydrogen bonds · protein-protein
- B–D · 1371 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 465 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 7JWK · Crystal Structure of Glyceraldehyde-3-phosphate Dehydrogenase (GAPDH) from Mycoplasma… · the same entry in another collection · chain D against D, TM-score 1.00
- P47543 · AlphaFold monomer V2.0 prediction for glyceraldehyde-3-phosphate dehydrogenase (P47543) · a predicted model of the same protein · chain D 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 P47543
- Elsewhere: RCSB PDB 7JWK · PDBe 7JWK · UniProt P47543
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.