Research workbench
Crystal structure of staphylococcal GAPDH1 in a hexagonal space group
Analyse Crystal structure of staphylococcal GAPDH1 in a hexagonal space group in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VAZ
- Type
- protein
- Length
- 2,005 residues
- Chains
- 6
- 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, DGY, PO4
- Pockets
- 15 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 25% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| P | Glyceraldehyde-3-phosphate dehydrogenase 1 (EC 1.2.1.12) | protein | 336 | 27% helix, 27% strand | Q6GIL8 |
| R, O, B, A | Glyceraldehyde-3-phosphate dehydrogenase 1 (EC 1.2.1.12) | protein | 334 | 25% helix, 29% strand | Q6GIL8 |
| Q | Glyceraldehyde-3-phosphate dehydrogenase 1 (EC 1.2.1.12) | protein | 333 | 25% helix, 31% strand | Q6GIL8 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 6 copies · chains P, Q, R, O, B, A
- DGY · (2R)-2,3-dihydroxypropanoic acid · ligand · 2 copies · chains O, A
- PO4 · Phosphate ion · ion · 6 copies · chains P, A, Q, O, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1123 | 0.82 | 0.83 | 95 | NAD |
| 2 | 714 | 0.74 | 0.79 | 69 | NAD |
| 3 | 499 | 0.73 | 0.82 | 57 | NAD |
| 4 | 512 | 0.72 | 0.81 | 59 | NAD |
| 5 | 584 | 0.71 | 0.80 | 60 | NAD |
Interfaces
10 interfaces between chains.
- B–A · 2200 Ų buried · 43 hydrogen bonds · protein-protein
- R–Q · 2144 Ų buried · 44 hydrogen bonds · protein-protein
- P–O · 2124 Ų buried · 46 hydrogen bonds · protein-protein
- R–O · 1498 Ų buried · 23 hydrogen bonds · protein-protein
- P–Q · 1455 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 3VAZ · Crystal structure of Staphylococcal GAPDH1 in a hexagonal space group · the same entry in another collection · chain A against A, 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 A 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 3VAZ · PDBe 3VAZ · UniProt Q6GIL8
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.