Research workbench
L-glutamate dehydrogenase from pyrobaculum islandicum complexed with NAD
Analyse L-glutamate dehydrogenase from pyrobaculum islandicum complexed with NAD in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1V9L
- Type
- protein
- Length
- 2,508 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate dehydrogenase
- EC
- 1.4.1.2
- UniProt
- Q9Y8I4
- Ligands
- NAD
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Glutamate dehydrogenase (EC 1.4.1.2) | protein | 418 | 48% helix, 16% strand | Q9Y8I4 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1056 | 0.86 | 0.87 | 88 | empty |
| 2 | 1051 | 0.86 | 0.87 | 89 | empty |
| 3 | 1056 | 0.86 | 0.87 | 79 | empty |
| 4 | 1104 | 0.78 | 0.80 | 108 | empty |
| 5 | 749 | 0.75 | 0.80 | 83 | empty |
Interfaces
12 interfaces between chains.
- A–F · 959 Ų buried · 12 hydrogen bonds · protein-protein
- B–E · 935 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 918 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 815 Ų buried · 12 hydrogen bonds · protein-protein
- D–E · 812 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 1V9L · L-glutamate dehydrogenase from Pyrobaculum islandicum complexed with NAD · the same entry in another collection · chain A 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 Q9Y8I4
- Elsewhere: RCSB PDB 1V9L · PDBe 1V9L · UniProt Q9Y8I4
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