Research workbench
Crystal structure of the small GTPase gem (gemdndcam) in complex to MG.GDP
Analyse Crystal structure of the small GTPase gem (gemdndcam) in complex to MG.GDP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2CJW
- Type
- protein
- Length
- 351 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTP-binding protein gem
- UniProt
- P55040
- Ligands
- GDP, MG
- Pockets
- 3 · best druggability 0.48
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GTP-binding protein gem | protein | 178 | 44% helix, 24% strand | P55040 |
| B | GTP-binding protein gem | protein | 173 | 43% helix, 25% strand | P55040 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 213 | 0.48 | 0.75 | 29 | empty |
| 2 | 100 | 0.38 | 0.75 | 18 | empty |
| 3 | 50 | 0.30 | 0.76 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 725 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 modified (artifact).
Compared structures
- 2CJW · Crystal structure of the small GTPase Gem (GemDNDCaM) in complex to Mg.GDP · the same entry in another collection · chain A against A, TM-score 1.00
- P55040 · AlphaFold monomer V2.0 prediction for GTP-binding protein gem (P55040) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 P55040
- Elsewhere: RCSB PDB 2CJW · PDBe 2CJW · UniProt P55040
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