Research workbench
Crystal structure of the guanylate cyclase domain of rhgc from catenaria anguillulae in complex with GTP
Analyse Crystal structure of the guanylate cyclase domain of rhgc from catenaria… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SIR
- Type
- protein
- Length
- 728 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleotide cyclase
- UniProt
- A0A1Y2HEJ3
- Ligands
- GTP, CA
- Pockets
- 2 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, C | Nucleotide cyclase | protein | 182 | 35% helix, 36% strand | A0A1Y2HEJ3 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 4 copies · chains A, B, D, C
- CA · Calcium ion · metal · 4 copies · chains A, B, D, C
- GOL · Glycerol · additive · 2 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 900 | 0.86 | 0.88 | 119 | GTP |
| 2 | 836 | 0.78 | 0.82 | 74 | CA, GTP |
Interfaces
6 interfaces between chains.
- A–B · 1445 Ų buried · 7 hydrogen bonds · protein-protein
- D–C · 1419 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 359 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 357 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 146 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6SIR · Crystal structure of the guanylate cyclase domain of RhGC from Catenaria anguillulae in… · 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 A0A1Y2HEJ3
- Elsewhere: RCSB PDB 6SIR · PDBe 6SIR · UniProt A0A1Y2HEJ3
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