Research workbench
Cleavage of nicotinamide adenine dinucleotides by the ribosome inactivating protein from momordica charantia
Analyse Cleavage of nicotinamide adenine dinucleotides by the ribosome inactivating… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YP2
- Type
- protein
- Length
- 246 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribosome-inactivating protein momordin I
- EC
- 3.2.2.22
- UniProt
- P16094
- Ligands
- NCA, NAG
- Pockets
- 2 · best druggability 0.47
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Ribosome-inactivating protein momordin I (EC 3.2.2.22) | protein | 246 | 41% helix, 25% strand | P16094 |
Ligands and binding sites
- NCA · Nicotinamide · ligand · chains B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 67 | 0.47 | 0.83 | 18 | NCA |
| 2 | 94 | 0.38 | 0.76 | 17 | empty |
Modifications
Observed in the structure: 1 glycan (N-glycosylation).
Compared structures
- 4YP2 · Cleavage of nicotinamide adenine dinucleotides by the ribosome inactivating protein from… · the same entry in another collection · chain B against B, TM-score 1.00
- P16094 · AlphaFold monomer V2.0 prediction for ribosome-inactivating protein momordin I (P16094) · a predicted model of the same protein · chain B 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 P16094
- Elsewhere: RCSB PDB 4YP2 · PDBe 4YP2 · UniProt P16094
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