Research workbench
Myxococcus xanthus mgla bound to GTP-gamma-S and mglb
Analyse Myxococcus xanthus mgla bound to GTP-gamma-S and mglb in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6IZW
- Type
- protein
- Length
- 462 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mutual gliding-motility protein mgla; Gliding motility protein mglb
- EC
- 3.6.5.2
- UniProt
- Q1DB04, Q1DB03
- Ligands
- GSP, MG, SO4
- Pockets
- 6 · best druggability 0.58
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mutual gliding-motility protein mgla (EC 3.6.5.2) | protein | 192 | 39% helix, 31% strand | Q1DB04 |
| B | Gliding motility protein mglb | protein | 145 | 43% helix, 25% strand | Q1DB03 |
| C | Gliding motility protein mglb | protein | 125 | 47% helix, 26% strand | Q1DB03 |
Ligands and binding sites
- GSP · 5'-guanosine-diphosphate-monothiophosphate · ligand · chains A
- MG · Magnesium ion · metal · chains A
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 131 | 0.58 | 0.84 | 30 | SO4 |
| 2 | 197 | 0.56 | 0.79 | 27 | empty |
| 3 | 136 | 0.43 | 0.76 | 28 | empty |
| 4 | 158 | 0.43 | 0.75 | 22 | empty |
| 5 | 66 | 0.42 | 0.81 | 20 | GSP, MG |
Interfaces
3 interfaces between chains.
- A–B · 1711 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 1095 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 518 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 modified (engineered).
Compared structures
- 6IZW · Myxococcus xanthus MglA bound to GTP-gamma-S and MglB · 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 0.95
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 Q1DB04
- Every structure of UniProt Q1DB03
- Elsewhere: RCSB PDB 6IZW · PDBe 6IZW · UniProt Q1DB04 · UniProt Q1DB03
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