Research workbench
Crystal structure of the human GDAP1 CMT2 mutant-H123R
Analyse Crystal structure of the human GDAP1 CMT2 mutant-H123R in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7Q6J
- Type
- protein
- Length
- 505 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ganglioside-induced differentiation-associated protein 1
- UniProt
- Q8TB36
- Pockets
- 8 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ganglioside-induced differentiation-associated protein 1 | protein | 257 | 52% helix, 7% strand | Q8TB36 |
| B | Ganglioside-induced differentiation-associated protein 1 | protein | 248 | 49% helix, 8% strand | Q8TB36 |
Ligands and binding sites
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 106 | 0.62 | 0.88 | 21 | empty |
| 2 | 257 | 0.61 | 0.81 | 38 | empty |
| 3 | 79 | 0.51 | 0.84 | 11 | empty |
| 4 | 58 | 0.43 | 0.83 | 14 | empty |
| 5 | 102 | 0.37 | 0.75 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 749 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7Q6J · Crystal structure of the human GDAP1 CMT2 mutant-H123R · the same entry in another collection · chain A against A, TM-score 1.00
- Q8TB36 · AlphaFold monomer V2.0 prediction for ganglioside-induced differentiation-associated… · a predicted model of the same protein · chain B against A, TM-score 0.89
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 Q8TB36
- Elsewhere: RCSB PDB 7Q6J · PDBe 7Q6J · UniProt Q8TB36
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