MolNFT v1 · #48349 · protein
Crystal structure of active ribosome inactivating protein from maize (B-32), complex with adenine
2PQJ · Ribosome-inactivating protein 3: “Crystal structure of active ribosome inactivating protein from maize (B-32), complex with adenine”. X-ray diffraction, 1 ligand (ADE), 3 pockets (best druggability 0.74). MolNFT v1 #48349 on…
- PDB
- 2PQJ
- Type
- protein
- Length
- 697 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribosome-inactivating protein 3
- EC
- 3.2.2.22
- UniProt
- P25891
- Ligands
- ADE
- Pockets
- 3 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribosome-inactivating protein 3 (EC 3.2.2.22) | protein | 233 | 39% helix, 15% strand | P25891 |
| B | Ribosome-inactivating protein 3 (EC 3.2.2.22) | protein | 232 | 39% helix, 17% strand | P25891 |
| C | Ribosome-inactivating protein 3 (EC 3.2.2.22) | protein | 232 | 36% helix, 14% strand | P25891 |
Ligands and binding sites
- ADE · Adenine · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1009 | 0.74 | 0.77 | 66 | ADE |
| 2 | 772 | 0.67 | 0.75 | 71 | ADE |
| 3 | 109 | 0.45 | 0.78 | 19 | ADE |
Interfaces
3 interfaces between chains.
- A–C · 232 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 160 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 18 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2PQJ · Crystal structure of active ribosome inactivating protein from maize (b-32), complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- P25891 · AlphaFold monomer V2.0 prediction for ribosome-inactivating protein 3 (P25891) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P25891
- Elsewhere: RCSB PDB 2PQJ · PDBe 2PQJ · UniProt P25891
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