MolNFT v1 · #149515 · protein
Crystal structure of the human glutamate dehydrogenase 2 (HGDH2)
6G2U · Glutamate dehydrogenase 2, mitochondrial: “Crystal structure of the human glutamate dehydrogenase 2 (HGDH2)”. X-ray diffraction, 3 ligands (NA, PO4, CL), 20 pockets (best druggability 0.88). MolNFT v1 #149515 on GenesisL1: 3D…
- PDB
- 6G2U
- Type
- protein
- Length
- 2,960 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate dehydrogenase 2, mitochondrial
- EC
- 1.4.1.3
- UniProt
- P49448
- Ligands
- NA, PO4, CL
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate dehydrogenase 2, mitochondrial (EC 1.4.1.3) | protein | 494 | 50% helix, 14% strand | P49448 |
| B, C | Glutamate dehydrogenase 2, mitochondrial (EC 1.4.1.3) | protein | 491 | 49% helix, 15% strand | P49448 |
| D, F | Glutamate dehydrogenase 2, mitochondrial (EC 1.4.1.3) | protein | 496 | 50% helix, 14% strand | P49448 |
| E | Glutamate dehydrogenase 2, mitochondrial (EC 1.4.1.3) | protein | 492 | 49% helix, 14% strand | P49448 |
Ligands and binding sites
- NA · Sodium ion · metal · 21 copies · chains A, C, D, B, E, F
- PO4 · Phosphate ion · ion · 23 copies · chains A, D, B, E, C, F
- CL · Chloride ion · ion · 19 copies · chains A, B, D, C, F, E
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 | 767 | 0.88 | 0.91 | 67 | PO4 |
| 2 | 1105 | 0.84 | 0.85 | 137 | PO4, CL, NA |
| 3 | 327 | 0.83 | 0.92 | 51 | empty |
| 4 | 827 | 0.77 | 0.81 | 86 | PO4 |
| 5 | 678 | 0.76 | 0.82 | 66 | PO4, NA |
Interfaces
10 interfaces between chains.
- B–D · 1781 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 1779 Ų buried · 20 hydrogen bonds · protein-protein
- C–F · 1755 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1746 Ų buried · 15 hydrogen bonds · protein-protein
- A–E · 476 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6G2U · Crystal structure of the human glutamate dehydrogenase 2 (hGDH2) · the same entry in another collection · chain F against F, TM-score 1.00
- P49448 · AlphaFold monomer V2.0 prediction for glutamate dehydrogenase 2, mitochondrial (P49448) · a predicted model of the same protein · chain E 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 P49448
- Elsewhere: RCSB PDB 6G2U · PDBe 6G2U · UniProt P49448
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