Research workbench
Cryo-EM MAP of the large glutamate dehydrogenase composed of 180 kda subunits from mycobacterium smegmatis (open conformation)
Analyse Cryo-EM MAP of the large glutamate dehydrogenase composed of 180 kda subunits… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7A1D
- Type
- protein
- Length
- 4,252 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD-specific glutamate dehydrogenase
- EC
- 1.4.1.2
- UniProt
- A0R1C2
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 1 distinct chain · 52% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | NAD-specific glutamate dehydrogenase (EC 1.4.1.2) | protein | 1063 | 52% helix, 9% strand | A0R1C2 |
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 | 667 | 0.81 | 0.86 | 68 | empty |
| 2 | 696 | 0.81 | 0.85 | 70 | empty |
| 3 | 533 | 0.78 | 0.85 | 56 | empty |
| 4 | 292 | 0.77 | 0.89 | 59 | empty |
| 5 | 507 | 0.76 | 0.84 | 51 | empty |
Interfaces
4 interfaces between chains.
- B–C · 1282 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 1245 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 588 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 585 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 7A1D · Cryo-EM map of the large glutamate dehydrogenase composed of 180 kDa subunits from… · the same entry in another collection · chain D against D, TM-score 1.00
- A0R1C2 · AlphaFold monomer V2.0 prediction for NAD-specific glutamate dehydrogenase (A0R1C2) · a predicted model of the same protein · chain C against A, TM-score 0.95
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 A0R1C2
- Elsewhere: RCSB PDB 7A1D · PDBe 7A1D · UniProt A0R1C2
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