Research workbench
Glyceraldehyde-3-phosphate dehydrogenase mutant with cys 149 replaced by ser complexed with NAD+ and D-glyceraldehyde-3-phosphate
Analyse Glyceraldehyde-3-phosphate dehydrogenase mutant with cys 149 replaced by ser… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NQO
- 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, G3H
- Pockets
- 13 · best druggability 0.73
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
- G3H · Glyceraldehyde-3-phosphate · ligand · 4 copies · chains O, Q, A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 649 | 0.73 | 0.80 | 82 | NAD, G3H |
| 2 | 654 | 0.69 | 0.77 | 60 | empty |
| 3 | 636 | 0.68 | 0.77 | 61 | NAD, G3H |
| 4 | 499 | 0.66 | 0.78 | 46 | NAD, G3H |
| 5 | 451 | 0.66 | 0.79 | 49 | NAD, G3H |
Interfaces
5 interfaces between chains.
- A–C · 577 Ų buried · 6 hydrogen bonds · protein-protein
- O–Q · 547 Ų buried · 6 hydrogen bonds · protein-protein
- Q–A · 264 Ų buried · 2 hydrogen bonds · protein-protein
- O–C · 253 Ų buried · 1 hydrogen bond · protein-protein
- Q–C · 205 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 1NQO · 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 1NQO · PDBe 1NQO · UniProt P00362
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