Research workbench
Myxococcus xanthus mgla in GDP bound conformation
Analyse Myxococcus xanthus mgla in GDP bound conformation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YMX
- Type
- protein
- Length
- 397 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mutual gliding-motility protein mgla
- EC
- 3.6.5.2
- UniProt
- Q1DB04
- Ligands
- GDP
- Pockets
- 5 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mutual gliding-motility protein mgla (EC 3.6.5.2) | protein | 202 | 36% helix, 27% strand | Q1DB04 |
| B | Mutual gliding-motility protein mgla (EC 3.6.5.2) | protein | 195 | 35% helix, 27% strand | Q1DB04 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
- IMD · Imidazole · additive · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 317 | 0.59 | 0.78 | 42 | empty |
| 2 | 247 | 0.55 | 0.77 | 25 | empty |
| 3 | 95 | 0.39 | 0.76 | 18 | empty |
| 4 | 70 | 0.33 | 0.75 | 17 | EDO |
| 5 | 62 | 0.33 | 0.76 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 382 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
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 5YMX · PDBe 5YMX · UniProt Q1DB04
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