Research workbench
Crystal structure of ggdef domain (I site mutant) from T. maritima
Analyse Crystal structure of ggdef domain (I site mutant) 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
- 4URQ
- Type
- protein
- Length
- 922 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Diguanylate cyclase
- UniProt
- Q9X2A8
- Pockets
- 9 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| U, W, X, Y | Diguanylate cyclase | protein | 154 | 49% helix, 25% strand | Q9X2A8 |
| V, Z | Diguanylate cyclase | protein | 153 | 49% helix, 25% strand | Q9X2A8 |
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 268 | 0.58 | 0.78 | 24 | empty |
| 2 | 239 | 0.57 | 0.79 | 25 | empty |
| 3 | 116 | 0.45 | 0.78 | 20 | empty |
| 4 | 66 | 0.41 | 0.80 | 13 | empty |
| 5 | 86 | 0.32 | 0.73 | 17 | empty |
Interfaces
6 interfaces between chains.
- V–X · 948 Ų buried · 23 hydrogen bonds · protein-protein
- U–Y · 944 Ų buried · 23 hydrogen bonds · protein-protein
- U–Z · 788 Ų buried · 16 hydrogen bonds · protein-protein
- V–W · 772 Ų buried · 16 hydrogen bonds · protein-protein
- U–X · 645 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4URQ · Crystal Structure of GGDEF domain (I site mutant) from T.maritima · the same entry in another collection · chain U against U, 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 4URQ · PDBe 4URQ · UniProt Q9X2A8
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