MolNFT v1 · #61284 · protein
Crystal structure of ribonuclease SA2 with guanosine-3'-cyclophosphate prepared by cocrystallization
3DH2: “Crystal structure of ribonuclease SA2 with guanosine-3'-cyclophosphate prepared by cocrystallization”. X-ray diffraction, 3 ligands (3GP, BGC, SO4), 5 pockets (best druggability 0.58). MolNFT v1 #61284 on GenesisL1: 3D structure…
- PDB
- 3DH2
- Type
- protein
- Length
- 380 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonuclease
- EC
- 3.1.4.8
- UniProt
- Q53752
- Ligands
- 3GP, BGC, SO4
- Pockets
- 5 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 15% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ribonuclease (EC 3.1.4.8) | protein | 94 | 15% helix, 26% strand | Q53752 |
| C, D | Ribonuclease (EC 3.1.4.8) | protein | 96 | 16% helix, 23% strand | Q53752 |
Ligands and binding sites
- 3GP · Guanosine-3'-monophosphate · ligand · 4 copies · chains A, B, C, D
- BGC · beta-D-glucopyranose · sugar · 3 copies · chains A, D, B, C
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 377 | 0.58 | 0.75 | 60 | SO4 |
| 2 | 51 | 0.33 | 0.78 | 15 | 3GP |
| 3 | 83 | 0.32 | 0.73 | 17 | empty |
| 4 | 55 | 0.30 | 0.75 | 14 | empty |
| 5 | 55 | 0.25 | 0.73 | 13 | empty |
Interfaces
5 interfaces between chains.
- A–C · 364 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 355 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 344 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 326 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 87 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 glycan (disulfide, glycosylation).
Compared structures
- 3DH2 · Crystal structure of ribonuclease Sa2 with guanosine-3'-cyclophosphate prepared by… · 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 Q53752
- Elsewhere: RCSB PDB 3DH2 · PDBe 3DH2 · UniProt Q53752
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