MolNFT v1 · #88989 · protein
Glyceraldehyde-3-phosphate dehydrogenase mutant with leu 33 replaced by thr, thr 34 replaced by gly, asp 36 replaced by gly, leu 187 replaced by ala, and pro 188 replaced by ser complexed with NADP+
4DBV: “Glyceraldehyde-3-phosphate dehydrogenase mutant with leu 33 replaced by thr, thr 34 replaced by gly, asp 36…”. X-ray diffraction, 2 ligands (NDP, SO4), 9 pockets (best druggability 0.78). MolNFT v1 #88989 on GenesisL1: 3D structure…
- PDB
- 4DBV
- 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
- 9 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 29% 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 | 29% helix, 30% strand | P00362 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains O, P, Q, R
- 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
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 992 | 0.78 | 0.80 | 113 | SO4, NDP |
| 2 | 102 | 0.76 | 0.97 | 29 | empty |
| 3 | 612 | 0.70 | 0.79 | 60 | SO4, NDP |
| 4 | 720 | 0.70 | 0.77 | 71 | SO4, NDP |
| 5 | 413 | 0.61 | 0.77 | 49 | empty |
Interfaces
6 interfaces between chains.
- Q–R · 2142 Ų buried · 36 hydrogen bonds · protein-protein
- O–P · 2133 Ų buried · 35 hydrogen bonds · protein-protein
- O–R · 1428 Ų buried · 19 hydrogen bonds · protein-protein
- P–Q · 1427 Ų buried · 20 hydrogen bonds · protein-protein
- P–R · 575 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4DBV · Glyceraldehyde-3-phosphate dehydrogenase mutant with leu 33 replaced by thr, thr 34… · 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 4DBV · PDBe 4DBV · UniProt P00362
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