MolNFT v1 · #62907 · protein
Glutamate dehydrogenase complexed with GW5074
3ETG: “Glutamate dehydrogenase complexed with GW5074”. X-ray diffraction, 4 ligands (GLU, NDP, GTP), 20 pockets (best druggability 0.87). MolNFT v1 #62907 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3ETG
- Type
- protein
- Length
- 3,006 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate dehydrogenase
- UniProt
- Q3SYY0
- Ligands
- GLU, NDP, GTP, GWD
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Glutamate dehydrogenase | protein | 501 | 48% helix, 13% strand | Q3SYY0 |
Ligands and binding sites
- GLU · Glutamic acid · ligand · 6 copies · chains A, B, C, D, E, F
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 6 copies · chains A, B, C, D, E, F
- GTP · Guanosine-5'-triphosphate · ligand · 6 copies · chains A, B, C, D, E, F
- GWD · (3E)-3-[(3,5-dibromo-4-hydroxyphenyl)methylidene]-5-iodo-1,3-dihydro-2H-indol-2-one · ligand · 6 copies · chains A, B, C, D, F, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1140 | 0.87 | 0.88 | 79 | empty |
| 2 | 1116 | 0.87 | 0.88 | 77 | empty |
| 3 | 773 | 0.86 | 0.90 | 95 | GWD |
| 4 | 726 | 0.86 | 0.90 | 83 | GWD |
| 5 | 534 | 0.84 | 0.90 | 70 | empty |
Interfaces
15 interfaces between chains.
- C–E · 1859 Ų buried · 24 hydrogen bonds · protein-protein
- B–F · 1851 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1842 Ų buried · 22 hydrogen bonds · protein-protein
- A–F · 1813 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1807 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 3ETG · Glutamate dehydrogenase complexed with GW5074 · the same entry in another collection · chain B against B, 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 Q3SYY0
- Elsewhere: RCSB PDB 3ETG · PDBe 3ETG · UniProt Q3SYY0
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