Research workbench
Crystal structure of C151G mutant of glyceraldehyde 3-phosphate dehydrogenase 1 (GAPDH1) from methicillin resistant staphylococcus aureus MRSA252 complexed with NAD and G3P
Analyse Crystal structure of C151G 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
- 3L4S
- 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
- 3PG, NAD
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 29% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| Q, O | Glyceraldehyde-3-phosphate dehydrogenase 1 (EC 1.2.1.12) | protein | 334 | 29% helix, 29% strand | Q6GIL8 |
| P | Glyceraldehyde-3-phosphate dehydrogenase 1 (EC 1.2.1.12) | protein | 333 | 29% helix, 29% strand | Q6GIL8 |
| R | Glyceraldehyde-3-phosphate dehydrogenase 1 (EC 1.2.1.12) | protein | 334 | 29% helix, 29% strand | Q6GIL8 |
Ligands and binding sites
- 3PG · 3-phosphoglyceric acid · ligand · 4 copies · chains Q, P, O, R
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains Q, P, O, R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1063 | 0.80 | 0.81 | 116 | NAD, 3PG |
| 2 | 583 | 0.74 | 0.82 | 70 | NAD, 3PG |
| 3 | 531 | 0.73 | 0.82 | 52 | 3PG, NAD |
| 4 | 483 | 0.68 | 0.79 | 67 | empty |
| 5 | 401 | 0.62 | 0.77 | 57 | empty |
Interfaces
6 interfaces between chains.
- Q–R · 2185 Ų buried · 48 hydrogen bonds · protein-protein
- P–O · 2183 Ų buried · 48 hydrogen bonds · protein-protein
- Q–P · 1496 Ų buried · 25 hydrogen bonds · protein-protein
- O–R · 1461 Ų buried · 22 hydrogen bonds · protein-protein
- Q–O · 636 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3L4S · Crystal structure of C151G mutant of Glyceraldehyde 3-phosphate dehydrogenase 1 (GAPDH1)… · the same entry in another collection · chain R against R, 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 3L4S · PDBe 3L4S · UniProt Q6GIL8
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