MolNFT v1 · #176043 · protein
Structure of huamn soluble guanylate cyclase in the YC1 and no-bound state
7D9S · Guanylate cyclase soluble subunit alpha-1: “Structure of huamn soluble guanylate cyclase in the YC1 and no-bound state”. Electron microscopy, 4 ligands (YC1, HEM, G2P), 13 pockets (best druggability 0.86). MolNFT v1 #176043 on…
- PDB
- 7D9S
- Type
- protein
- Length
- 1,071 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
- YC1, HEM, G2P, MG
- Pockets
- 13 · best druggability 0.86
Structure
electron microscopy · 2 distinct chains · 43% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Guanylate cyclase soluble subunit alpha-1 (EC 4.6.1.2) | protein | 502 | 43% helix, 17% strand | Q02108 |
| B | Guanylate cyclase soluble subunit beta-1 (EC 4.6.1.2) | protein | 569 | 43% helix, 20% strand | Q02153 |
Ligands and binding sites
- YC1 · [5-[1-(phenylmethyl)indazol-3-yl]furan-2-yl]methanol · ligand · chains A, B
- HEM · Protoporphyrin IX containing Fe · ligand · chains A, B
- G2P · Phosphomethylphosphonic acid guanylate ester · 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 689 | 0.86 | 0.89 | 57 | YC1, HEM |
| 2 | 747 | 0.76 | 0.81 | 65 | MG, G2P |
| 3 | 54 | 0.71 | 0.98 | 23 | empty |
| 4 | 360 | 0.68 | 0.81 | 32 | empty |
| 5 | 239 | 0.57 | 0.79 | 43 | empty |
Interfaces
1 interface between chains.
- A–B · 6118 Ų buried · 34 hydrogen bonds · protein-protein
Compared structures
- 7D9S · Structure of huamn soluble guanylate cyclase in the YC1 and NO-bound 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 0.66
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 7D9S · PDBe 7D9S · UniProt Q02108 · UniProt Q02153
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