MolNFT v1 · #34301 · protein
Glyceraldehyde-3-phosphate dehydrogenase mutant with asp 32 replaced by gly, leu 187 replaced by ala, and pro 188 replaced by ser complexed with NADP+
2DBV: “Glyceraldehyde-3-phosphate dehydrogenase mutant with asp 32 replaced by gly, leu 187 replaced by ala, and pro…”. X-ray diffraction, 2 ligands (NDP, SO4), 14 pockets (best druggability 0.76). MolNFT v1 #34301 on GenesisL1: 3D…
- PDB
- 2DBV
- 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
- NDP, SO4
- Pockets
- 14 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 28% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| O, P, Q, R | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) | protein | 334 | 28% helix, 30% strand | P00362 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains O, R, P, Q
- SO4 · Sulfate ion · ion · 8 copies · chains O, P, Q, R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 94 | 0.76 | 0.98 | 29 | empty |
| 2 | 711 | 0.71 | 0.78 | 62 | SO4, NDP |
| 3 | 650 | 0.70 | 0.78 | 54 | SO4, NDP |
| 4 | 660 | 0.70 | 0.78 | 65 | SO4, NDP |
| 5 | 648 | 0.69 | 0.78 | 58 | SO4, NDP |
Interfaces
6 interfaces between chains.
- Q–R · 2121 Ų buried · 38 hydrogen bonds · protein-protein
- O–P · 2095 Ų buried · 35 hydrogen bonds · protein-protein
- P–Q · 1428 Ų buried · 23 hydrogen bonds · protein-protein
- O–R · 1419 Ų buried · 16 hydrogen bonds · protein-protein
- P–R · 590 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 2DBV · Glyceraldehyde-3-phosphate dehydrogenase mutant with asp 32 replaced by gly, leu 187… · the same entry in another collection · chain R against R, TM-score 1.00
- P00362 · AlphaFold monomer V2.0 prediction for glyceraldehyde-3-phosphate dehydrogenase (P00362) · a predicted model of the same protein · chain R 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 P00362
- Elsewhere: RCSB PDB 2DBV · PDBe 2DBV · UniProt P00362
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.