MolNFT v1 · #16146 · protein
Glyceraldehyde-3-phosphate dehydrogenase mutant with cys 149 replaced by ser complexed with NAD+
1NQ5 · Glyceraldehyde 3-phosphate dehydrogenase: “Glyceraldehyde-3-phosphate dehydrogenase mutant with cys 149 replaced by ser complexed with NAD+”. X-ray diffraction, 2 ligands (NAD, SO4), 10 pockets (best druggability 0.72). MolNFT v1…
- PDB
- 1NQ5
- 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
- EC
- 1.2.1.12
- UniProt
- P00362
- Ligands
- NAD, SO4
- Pockets
- 10 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| O, Q, A, C | Glyceraldehyde 3-phosphate dehydrogenase (EC 1.2.1.12) | protein | 334 | 30% helix, 30% strand | P00362 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains O, Q, A, C
- SO4 · Sulfate ion · ion · 4 copies · chains O, Q, A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 784 | 0.72 | 0.78 | 81 | SO4, NAD |
| 2 | 699 | 0.69 | 0.77 | 58 | empty |
| 3 | 572 | 0.68 | 0.78 | 55 | SO4, NAD |
| 4 | 621 | 0.68 | 0.77 | 59 | SO4, NAD |
| 5 | 605 | 0.68 | 0.77 | 55 | SO4, NAD |
Interfaces
5 interfaces between chains.
- A–C · 597 Ų buried · 6 hydrogen bonds · protein-protein
- O–Q · 574 Ų buried · 4 hydrogen bonds · protein-protein
- Q–A · 216 Ų buried · 1 hydrogen bond · protein-protein
- Q–C · 206 Ų buried · 1 hydrogen bond · protein-protein
- O–C · 185 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 1NQ5 · Glyceraldehyde-3-Phosphate Dehydrogenase Mutant With Cys 149 Replaced By Ser Complexed… · the same entry in another collection · chain C against C, TM-score 1.00
- P00362 · AlphaFold monomer V2.0 prediction for glyceraldehyde-3-phosphate dehydrogenase (P00362) · a predicted model of the same protein · chain C 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 P00362
- Elsewhere: RCSB PDB 1NQ5 · PDBe 1NQ5 · UniProt P00362
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