Research workbench
Crystal structure of C151S mutant of glyceraldehyde-3-phosphate dehydrogenase 1 (GAPDH1) complexed with NAD from staphylococcus aureus MRSA252 at 2.2 ångström resolution
Analyse Crystal structure of C151S mutant of glyceraldehyde-3-phosphate dehydrogenase 1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HQ4
- Type
- protein
- Length
- 1,336 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
- Pockets
- 14 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 28% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| R, O, P, Q | Glyceraldehyde-3-phosphate dehydrogenase 1 (EC 1.2.1.12) | protein | 334 | 28% helix, 29% strand | Q6GIL8 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains R, O, P, Q
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1114 | 0.80 | 0.82 | 106 | NAD |
| 2 | 624 | 0.74 | 0.81 | 70 | NAD |
| 3 | 539 | 0.73 | 0.81 | 53 | NAD |
| 4 | 519 | 0.70 | 0.80 | 66 | empty |
| 5 | 346 | 0.62 | 0.78 | 53 | empty |
Interfaces
6 interfaces between chains.
- O–P · 2166 Ų buried · 45 hydrogen bonds · protein-protein
- R–Q · 2095 Ų buried · 50 hydrogen bonds · protein-protein
- P–Q · 1483 Ų buried · 27 hydrogen bonds · protein-protein
- R–O · 1481 Ų buried · 27 hydrogen bonds · protein-protein
- O–Q · 582 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3HQ4 · Crystal Structure of C151S mutant of Glyceraldehyde-3-phosphate dehydrogenase 1 (GAPDH1)… · 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 O 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 3HQ4 · PDBe 3HQ4 · UniProt Q6GIL8
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.