MolNFT v1 · #176045 · protein
Structure of human soluble guanylate cyclase in the cinciguat-bound activated state
7D9U · Guanylate cyclase soluble subunit alpha-1: “Structure of human soluble guanylate cyclase in the cinciguat-bound activated state”. Electron microscopy, 3 ligands (G2P, Z90, MG), 13 pockets (best druggability 0.86). MolNFT v1 #176045…
- PDB
- 7D9U
- Type
- protein
- Length
- 1,075 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Guanylate cyclase soluble subunit alpha-1; Guanylate cyclase soluble subunit beta-1
- EC
- 4.6.1.2
- UniProt
- Q02108, Q02153
- Ligands
- G2P, Z90, MG
- Pockets
- 13 · best druggability 0.86
Structure
electron microscopy · 2 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Guanylate cyclase soluble subunit alpha-1 (EC 4.6.1.2) | protein | 506 | 43% helix, 14% strand | Q02108 |
| B | Guanylate cyclase soluble subunit beta-1 (EC 4.6.1.2) | protein | 569 | 43% helix, 19% strand | Q02153 |
Ligands and binding sites
- G2P · Phosphomethylphosphonic acid guanylate ester · ligand · chains A, B
- Z90 · 4-({(4-carboxybutyl)[2-(2-{[4-(2-phenylethyl) benzyl]oxy}phenyl)ethyl]amino}methyl)benzoic acid · ligand · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 434 | 0.86 | 0.92 | 37 | Z90 |
| 2 | 703 | 0.77 | 0.82 | 61 | G2P, MG |
| 3 | 405 | 0.67 | 0.80 | 35 | empty |
| 4 | 199 | 0.56 | 0.79 | 41 | empty |
| 5 | 234 | 0.55 | 0.77 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 6043 Ų buried · 38 hydrogen bonds · protein-protein
Compared structures
- 7D9U · Structure of human soluble guanylate cyclase in the cinciguat-bound activated state · the same entry in another collection · chain A against A, TM-score 1.00
- Q02153 · AlphaFold monomer V2.0 prediction for guanylate cyclase soluble subunit beta-1 (Q02153) · a predicted model of the same protein · chain B against A, TM-score 0.77
- Q02108 · AlphaFold monomer V2.0 prediction for guanylate cyclase soluble subunit alpha-1 (Q02108) · a predicted model of the same protein · chain A against A, TM-score 0.65
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 Q02108
- Every structure of UniProt Q02153
- Elsewhere: RCSB PDB 7D9U · PDBe 7D9U · UniProt Q02108 · UniProt Q02153
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