MolNFT v1 · #61010 · protein
RNase a- 5'-deoxy-5'-N-pyrrolidinothymidine complex
3D8Z · Ribonuclease pancreatic: “RNase a- 5'-deoxy-5'-N-pyrrolidinothymidine complex”. X-ray diffraction, 1 ligand (TXS), 3 pockets (best druggability 0.36). MolNFT v1 #61010 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3D8Z
- Type
- protein
- Length
- 248 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonuclease pancreatic
- EC
- 3.1.27.5
- UniProt
- P61823
- Ligands
- TXS
- Pockets
- 3 · best druggability 0.36
Structure
x-ray diffraction · 1 distinct chain · 21% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ribonuclease pancreatic (EC 3.1.27.5) | protein | 124 | 21% helix, 35% strand | P61823 |
Ligands and binding sites
- TXS · 1-(2,5-dideoxy-5-pyrrolidin-1-yl-beta-L-erythro-pentofuranosyl)-5-methylpyrimidine-2,4(1H,3H)-dione · ligand · chains A
- FLC · Citrate anion · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 69 | 0.36 | 0.78 | 14 | empty |
| 2 | 51 | 0.32 | 0.78 | 12 | empty |
| 3 | 71 | 0.30 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 344 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 3D8Z · RNase A- 5'-Deoxy-5'-N-pyrrolidinothymidine complex · 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 P61823
- Elsewhere: RCSB PDB 3D8Z · PDBe 3D8Z · UniProt P61823
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