MolNFT v1 · #172269 · protein
Diguanylate cyclase dgcr (I-site mutant) in activated state
6ZXC · Putative GGDEF/RESPONSE regulator receiver domain protein: “Diguanylate cyclase dgcr (I-site mutant) in activated state”. X-ray diffraction, 2 ligands (GH3, MG), 11 pockets (best druggability 0.69). MolNFT v1 #172269 on GenesisL1…
- PDB
- 6ZXC
- Type
- protein
- Length
- 1,172 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative GGDEF/RESPONSE regulator receiver domain protein
- UniProt
- B0SUI1
- Ligands
- GH3, MG
- Pockets
- 11 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Putative GGDEF/RESPONSE regulator receiver domain protein | protein | 293 | 49% helix, 21% strand | B0SUI1 |
Ligands and binding sites
- GH3 · 3'-deoxy-guanosine-5'-triphosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 12 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 786 | 0.69 | 0.76 | 73 | GH3, MG |
| 2 | 545 | 0.64 | 0.76 | 42 | GH3 |
| 3 | 376 | 0.61 | 0.77 | 51 | empty |
| 4 | 255 | 0.54 | 0.76 | 32 | empty |
| 5 | 212 | 0.52 | 0.77 | 28 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1327 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1252 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 442 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 68 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 13 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nonstandard).
Compared structures
- 6ZXC · Diguanylate cyclase DgcR (I-site mutant) in activated state · 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 B0SUI1
- Elsewhere: RCSB PDB 6ZXC · PDBe 6ZXC · UniProt B0SUI1
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