Research workbench
Crystal structure of glutamate dehydrogenase (gdhb) from thermus thermophilus (glu bound form)
Analyse Crystal structure of glutamate dehydrogenase (gdhb) from thermus thermophilus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3AOG
- Type
- protein
- Length
- 5,047 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate dehydrogenase
- EC
- 1.4.1.3
- UniProt
- Q72IC1
- Ligands
- GLU, PO4, NH4
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, L | Glutamate dehydrogenase (EC 1.4.1.3) | protein | 421 | 49% helix, 16% strand | Q72IC1 |
| K | Glutamate dehydrogenase (EC 1.4.1.3) | protein | 416 | 47% helix, 17% strand | Q72IC1 |
Ligands and binding sites
- GLU · Glutamic acid · ligand · 24 copies · chains A, B, E, D, C, F, G, I, J, H, L, K
- PO4 · Phosphate ion · ion · 9 copies · chains A, C, E, B, D, F, G, H, I, J, L, K
- NH4 · Ammonium ion · ion · 6 copies · chains A, E, B, F, H, J, L
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 | 784 | 0.86 | 0.89 | 90 | GLU |
| 2 | 783 | 0.86 | 0.89 | 92 | GLU |
| 3 | 1116 | 0.85 | 0.86 | 127 | empty |
| 4 | 1145 | 0.85 | 0.86 | 131 | empty |
| 5 | 1128 | 0.85 | 0.86 | 137 | empty |
Interfaces
35 interfaces between chains.
- A–B · 1732 Ų buried · 21 hydrogen bonds · protein-protein
- I–K · 1701 Ų buried · 24 hydrogen bonds · protein-protein
- G–J · 1688 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1662 Ų buried · 22 hydrogen bonds · protein-protein
- E–F · 1642 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 3AOG · Crystal structure of glutamate dehydrogenase (GdhB) from Thermus thermophilus (Glu bound… · 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 Q72IC1
- Elsewhere: RCSB PDB 3AOG · PDBe 3AOG · UniProt Q72IC1
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