Research workbench
Crystal structure of phosphate bound apo glyceraldehyde-3-phosphate dehydrogenase 1 from MRSA252 at 2.2 ångström resolution
Analyse Crystal structure of phosphate bound apo glyceraldehyde-3-phosphate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3L6O
- 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
- PO4
- Pockets
- 8 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| Q, P, R | Glyceraldehyde-3-phosphate dehydrogenase 1 (EC 1.2.1.12) | protein | 334 | 26% helix, 28% strand | Q6GIL8 |
| O | Glyceraldehyde-3-phosphate dehydrogenase 1 (EC 1.2.1.12) | protein | 333 | 28% helix, 29% strand | Q6GIL8 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 4 copies · chains Q, P, R, O
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 | 990 | 0.80 | 0.82 | 106 | PO4 |
| 2 | 778 | 0.75 | 0.80 | 116 | empty |
| 3 | 529 | 0.73 | 0.82 | 59 | PO4 |
| 4 | 464 | 0.72 | 0.82 | 53 | PO4 |
| 5 | 92 | 0.47 | 0.81 | 20 | empty |
Interfaces
6 interfaces between chains.
- P–O · 2209 Ų buried · 41 hydrogen bonds · protein-protein
- Q–R · 2188 Ų buried · 49 hydrogen bonds · protein-protein
- Q–P · 1504 Ų buried · 30 hydrogen bonds · protein-protein
- R–O · 1500 Ų buried · 29 hydrogen bonds · protein-protein
- Q–O · 629 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3L6O · Crystal Structure of Phosphate bound apo Glyceraldehyde-3-phosphate dehydrogenase 1 from… · the same entry in another collection · chain O against O, 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 0.99
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 3L6O · PDBe 3L6O · UniProt Q6GIL8
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