Research workbench
Crystal structure of the catalytic domain of the heterodimeric human soluble guanylate cyclase 1.
Analyse Crystal structure of the catalytic domain of the heterodimeric human soluble… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3UVJ
- Type
- protein
- Length
- 774 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Guanylate cyclase soluble subunit alpha-3; Guanylate cyclase soluble subunit beta-1
- EC
- 4.6.1.2
- UniProt
- Q02108, Q02153
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Guanylate cyclase soluble subunit alpha-3 (EC 4.6.1.2) | protein | 191 | 33% helix, 32% strand | Q02108 |
| B | Guanylate cyclase soluble subunit beta-1 (EC 4.6.1.2) | protein | 196 | 32% helix, 34% strand | Q02153 |
| C | Guanylate cyclase soluble subunit alpha-3 (EC 4.6.1.2) | protein | 191 | 33% helix, 32% strand | Q02108 |
| D | Guanylate cyclase soluble subunit beta-1 (EC 4.6.1.2) | protein | 196 | 32% helix, 34% strand | Q02153 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B, D, C
- GOL · Glycerol · additive · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1037 | 0.75 | 0.78 | 92 | GOL |
| 2 | 562 | 0.74 | 0.81 | 57 | GOL |
| 3 | 548 | 0.73 | 0.81 | 53 | empty |
| 4 | 470 | 0.71 | 0.81 | 49 | EDO |
Interfaces
4 interfaces between chains.
- C–D · 1318 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1279 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 380 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 54 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3UVJ · Crystal structure of the catalytic domain of the heterodimeric human soluble guanylate… · the same entry in another collection · chain D against D, 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 0.97
- 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 0.96
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 3UVJ · PDBe 3UVJ · UniProt Q02108 · UniProt Q02153
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