Research workbench
Crystal structure of bovine glutamate dehydrogenase-ADP complex
Analyse Crystal structure of bovine glutamate dehydrogenase-ADP complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NQT
- Type
- protein
- Length
- 5,952 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate dehydrogenase 1
- EC
- 1.4.1.3
- UniProt
- P00366
- Ligands
- ADP
- Pockets
- 20 · best druggability 0.91
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | Glutamate dehydrogenase 1 (EC 1.4.1.3) | protein | 496 | 45% helix, 12% strand | P00366 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 12 copies · chains A, B, F, C, D, E, G, H, L, I, J, K
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 | 1012 | 0.91 | 0.93 | 127 | empty |
| 2 | 1155 | 0.91 | 0.93 | 130 | ADP |
| 3 | 941 | 0.91 | 0.93 | 103 | empty |
| 4 | 1200 | 0.91 | 0.93 | 141 | ADP |
| 5 | 1077 | 0.91 | 0.93 | 121 | empty |
Interfaces
37 interfaces between chains.
- C–D · 1861 Ų buried · 27 hydrogen bonds · protein-protein
- G–H · 1845 Ų buried · 30 hydrogen bonds · protein-protein
- A–F · 1841 Ų buried · 23 hydrogen bonds · protein-protein
- I–K · 1803 Ų buried · 23 hydrogen bonds · protein-protein
- G–L · 1798 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 1NQT · Crystal structure of bovine Glutamate dehydrogenase-ADP complex · the same entry in another collection · chain L against L, 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 P00366
- Elsewhere: RCSB PDB 1NQT · PDBe 1NQT · UniProt P00366
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