MolNFT v1 · #155729 · protein
Crystal structure of an oxido-reductase with mutation and inhibitor
6LGM · Glyceraldehyde-3-phosphate dehydrogenase: “Crystal structure of an oxido-reductase with mutation and inhibitor”. X-ray diffraction, 3 ligands (NAD, 9HB, PO4), 10 pockets (best druggability 0.81). MolNFT v1 #155729 on GenesisL1: 3D…
- PDB
- 6LGM
- Type
- protein
- Length
- 1,332 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, 2.6.99.-
- UniProt
- P16858
- Ligands
- NAD, 9HB, PO4
- Pockets
- 10 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12, 2.6.99.-) | protein | 333 | 33% helix, 26% strand | P16858 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 3 copies · chains A, C, B, D
- 9HB · Dimethyl fumarate · ligand · 3 copies · chains A, B, C
- PO4 · Phosphate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 953 | 0.81 | 0.82 | 122 | empty |
| 2 | 672 | 0.70 | 0.78 | 61 | NAD, PO4, 9HB |
| 3 | 610 | 0.69 | 0.78 | 65 | NAD, PO4, 9HB |
| 4 | 622 | 0.69 | 0.78 | 57 | PO4 |
| 5 | 613 | 0.69 | 0.78 | 57 | NAD, PO4, 9HB |
Interfaces
6 interfaces between chains.
- B–C · 2030 Ų buried · 29 hydrogen bonds · protein-protein
- A–D · 2029 Ų buried · 32 hydrogen bonds · protein-protein
- A–C · 1402 Ų buried · 24 hydrogen bonds · protein-protein
- B–D · 1372 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 502 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6LGM · Crystal structure of an oxido-reductase with mutation and inhibitor · the same entry in another collection · chain D against D, TM-score 1.00
- P16858 · AlphaFold monomer V2.0 prediction for glyceraldehyde-3-phosphate dehydrogenase (P16858) · a predicted model of the same protein · chain C 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 P16858
- Elsewhere: RCSB PDB 6LGM · PDBe 6LGM · UniProt P16858
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