MolNFT v1 · #69521 · protein
Crystal structure of C151S+H178N mutant of glyceraldehyde-3-phosphate- dehydrogenase 1 (GAPDH 1) from staphylococcus aureus MRSA252 complexed with NAD and G3P
3KSZ · Glyceraldehyde-3-phosphate dehydrogenase 1: “Crystal structure of C151S+H178N mutant of glyceraldehyde-3-phosphate- dehydrogenase 1 (GAPDH 1) from…”. X-ray diffraction, 2 ligands (NAD, 3PG), 12 pockets (best druggability 0.80).…
- PDB
- 3KSZ
- Type
- protein
- Length
- 1,335 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glyceraldehyde-3-phosphate dehydrogenase 1
- EC
- 1.2.1.12
- UniProt
- Q6GIL8
- Ligands
- NAD, 3PG
- Pockets
- 12 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| O, P, R | Glyceraldehyde-3-phosphate dehydrogenase 1 (EC 1.2.1.12) | protein | 334 | 31% helix, 29% strand | Q6GIL8 |
| Q | Glyceraldehyde-3-phosphate dehydrogenase 1 (EC 1.2.1.12) | protein | 333 | 31% helix, 29% strand | Q6GIL8 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains O, R, P, Q
- 3PG · 3-phosphoglyceric acid · ligand · 4 copies · chains O, P, R, Q
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1170 | 0.80 | 0.82 | 113 | NAD, 3PG |
| 2 | 920 | 0.76 | 0.79 | 113 | empty |
| 3 | 446 | 0.74 | 0.84 | 60 | NAD, 3PG |
| 4 | 384 | 0.72 | 0.84 | 48 | NAD, 3PG |
| 5 | 81 | 0.44 | 0.81 | 18 | empty |
Interfaces
6 interfaces between chains.
- R–Q · 2235 Ų buried · 50 hydrogen bonds · protein-protein
- O–P · 2193 Ų buried · 53 hydrogen bonds · protein-protein
- P–Q · 1503 Ų buried · 22 hydrogen bonds · protein-protein
- O–R · 1470 Ų buried · 26 hydrogen bonds · protein-protein
- O–Q · 613 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3KSZ · Crystal Structure of C151S+H178N mutant of Glyceraldehyde-3-phosphate-dehydrogenase 1… · the same entry in another collection · chain Q against Q, 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 R 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 3KSZ · PDBe 3KSZ · UniProt Q6GIL8
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