MolNFT v1 · #163953 · protein
Crystal structure of the guanylate cyclase domain of rhgc from catenaria anguillulae in complex with GTP
6SIR · Nucleotide cyclase: “Crystal structure of the guanylate cyclase domain of rhgc from catenaria anguillulae in complex with GTP”. X-ray diffraction, 2 ligands (GTP, CA), 2 pockets (best druggability 0.86). MolNFT v1 #163953 on…
- 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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