Research workbench
Structure of the hybrid domain (ggdef-eal) of PA0575 from pseudomonas aeruginosa PAO1 at 2.8 ang. with GTP and CA2+ bound to the active site of the ggdef domain
Analyse Structure of the hybrid domain (ggdef-eal) of PA0575 from pseudomonas… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5M3C
- Type
- protein
- Length
- 846 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Diguanylate cyclase
- UniProt
- A0A140SCF9
- Ligands
- GTP, CA
- Pockets
- 6 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Diguanylate cyclase | protein | 420 | 46% helix, 22% strand | A0A140SCF9 |
| B | Diguanylate cyclase | protein | 426 | 48% helix, 23% strand | A0A140SCF9 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 5 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1161 | 0.72 | 0.76 | 88 | CA |
| 2 | 446 | 0.68 | 0.80 | 44 | empty |
| 3 | 56 | 0.67 | 0.95 | 19 | empty |
| 4 | 306 | 0.58 | 0.77 | 38 | CA |
| 5 | 147 | 0.46 | 0.76 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1501 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5M3C · Structure of the hybrid domain (GGDEF-EAL) of PA0575 from Pseudomonas aeruginosa PAO1 at… · the same entry in another collection · chain A against A, TM-score 1.00
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 A0A140SCF9
- Elsewhere: RCSB PDB 5M3C · PDBe 5M3C · UniProt A0A140SCF9
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