Research workbench
Crystal structure of aspergillus niger glutamate dehydrogenase complexed with alpha-iminoglutarate, 2-amino-2-hydroxyglutarate and NADP
Analyse Crystal structure of aspergillus niger glutamate dehydrogenase complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XWC
- Type
- protein
- Length
- 459 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate dehydrogenase
- UniProt
- B6V7E4
- Ligands
- NAP, 8GL, 2IT
- Pockets
- 2 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate dehydrogenase | protein | 459 | 45% helix, 15% strand | B6V7E4 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · chains A
- 8GL · (2S)-2-azanyl-2-oxidanyl-pentanedioic acid · ligand · chains A
- 2IT · (2Z)-2-iminopentanedioic acid · ligand · chains A
- GOL · Glycerol · additive · 49 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 732 | 0.79 | 0.84 | 69 | NAP, 8GL, 2IT, GOL |
| 2 | 79 | 0.30 | 0.73 | 18 | GOL |
Compared structures
- 5XWC · Crystal Structure of Aspergillus niger Glutamate Dehydrogenase Complexed With… · 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 B6V7E4
- Elsewhere: RCSB PDB 5XWC · PDBe 5XWC · UniProt B6V7E4
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