MolNFT v1 · #69593 · protein
Crystal structure of C151S mutant of glyceraldehyde-3-phosphate dehydrogenase 1 (GAPDH 1)FROM methicillin resistant staphylococcus aureus MRSA252 complexed with NAD and G3P
3KV3: “Crystal structure of C151S mutant of glyceraldehyde-3-phosphate dehydrogenase 1 (GAPDH 1)FROM methicillin…”. X-ray diffraction, 2 ligands (NAD, 3PG), 8 pockets (best druggability 0.80). MolNFT v1 #69593 on GenesisL1: 3D structure…
- PDB
- 3KV3
- Type
- protein
- Length
- 1,336 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GAPDH
- EC
- 1.2.1.12
- UniProt
- Q6GIL8
- Ligands
- NAD, 3PG
- Pockets
- 8 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| O, Q, R, P | GAPDH (EC 1.2.1.12) | protein | 334 | 29% helix, 29% strand | Q6GIL8 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains O, R, Q, P
- 3PG · 3-phosphoglyceric acid · ligand · 4 copies · chains O, Q, R, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1103 | 0.80 | 0.82 | 113 | NAD, 3PG |
| 2 | 1143 | 0.80 | 0.81 | 129 | NAD, 3PG |
| 3 | 457 | 0.68 | 0.80 | 70 | empty |
| 4 | 380 | 0.61 | 0.77 | 62 | empty |
| 5 | 102 | 0.49 | 0.82 | 20 | empty |
Interfaces
6 interfaces between chains.
- Q–R · 2190 Ų buried · 47 hydrogen bonds · protein-protein
- O–P · 2184 Ų buried · 45 hydrogen bonds · protein-protein
- O–R · 1491 Ų buried · 24 hydrogen bonds · protein-protein
- Q–P · 1474 Ų buried · 21 hydrogen bonds · protein-protein
- R–P · 611 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3KV3 · Crystal structure of C151S mutant of Glyceraldehyde-3-phosphate dehydrogenase 1 (GAPDH… · the same entry in another collection · chain P against P, TM-score 1.00
- Q6GIL8 · AlphaFold monomer V2.0 prediction for glyceraldehyde-3-phosphate dehydrogenase 1 (Q6GIL8) · a predicted model of the same protein · chain P 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 Q6GIL8
- Elsewhere: RCSB PDB 3KV3 · PDBe 3KV3 · UniProt Q6GIL8
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.