Research workbench
Myxococcus xanthus mgla bound to GDP and pi with mixed inactive and active switch region conformations
Analyse Myxococcus xanthus mgla bound to GDP and pi with mixed inactive and active… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6H35
- Type
- protein
- Length
- 386 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mutual gliding-motility protein mgla
- UniProt
- Q1DB04
- Ligands
- GDP, PO4
- Pockets
- 8 · best druggability 0.44
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Mutual gliding-motility protein mgla | protein | 193 | 36% helix, 27% strand | Q1DB04 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 9 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 117 | 0.44 | 0.76 | 19 | empty |
| 2 | 97 | 0.41 | 0.77 | 15 | empty |
| 3 | 100 | 0.39 | 0.76 | 15 | empty |
| 4 | 77 | 0.39 | 0.77 | 17 | empty |
| 5 | 80 | 0.36 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 410 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6H35 · Myxococcus xanthus MglA bound to GDP and Pi with mixed inactive and active switch region… · the same entry in another collection · chain A against A, TM-score 1.00
- Q1DB04 · AlphaFold monomer V2.0 prediction for mutual gliding-motility protein mgla (Q1DB04) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q1DB04
- Elsewhere: RCSB PDB 6H35 · PDBe 6H35 · UniProt Q1DB04
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