Research workbench
Crystal structure of ggdef domain from T.MARITIMA
Analyse Crystal structure of ggdef domain from T.MARITIMA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4URS
- Type
- protein
- Length
- 324 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Diguanylate cyclase
- UniProt
- Q9X2A8
- Ligands
- C2E
- Pockets
- 2 · best druggability 0.32
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Diguanylate cyclase | protein | 162 | 47% helix, 23% strand | Q9X2A8 |
Ligands and binding sites
- C2E · 9,9'-[(2r,3r,3as,5s,7ar,9r,10r,10as,12s,14ar)-3,5,10, 12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3, 2-D:3',2'-J][1,3,7,9,2, 8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) · ligand · 4 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 66 | 0.32 | 0.76 | 17 | empty |
| 2 | 73 | 0.31 | 0.74 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1341 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
- 4URS · Crystal Structure of GGDEF domain from T.maritima · 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 Q9X2A8
- Elsewhere: RCSB PDB 4URS · PDBe 4URS · UniProt Q9X2A8
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