MolNFT v1 · #69557 · protein
Structure of GAP31 with adenine at its binding pocket
3KU0 · Ribosome-inactivating protein gelonin: “Structure of GAP31 with adenine at its binding pocket”. X-ray diffraction, 2 ligands (ADE, NAG), 4 pockets (best druggability 0.70). MolNFT v1 #69557 on GenesisL1: 3D structure, binding sites…
- PDB
- 3KU0
- Type
- protein
- Length
- 502 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribosome-inactivating protein gelonin
- EC
- 3.2.2.22
- UniProt
- P33186
- Ligands
- ADE, NAG
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ribosome-inactivating protein gelonin (EC 3.2.2.22) | protein | 251 | 37% helix, 24% strand | P33186 |
Ligands and binding sites
- ADE · Adenine · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 359 | 0.70 | 0.82 | 50 | empty |
| 2 | 202 | 0.49 | 0.75 | 37 | ADE |
| 3 | 125 | 0.46 | 0.78 | 21 | ADE |
| 4 | 74 | 0.43 | 0.80 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1012 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 3KU0 · Structure of GAP31 with adenine at its binding pocket · the same entry in another collection · chain A against A, TM-score 1.00
- P33186 · AlphaFold monomer V2.0 prediction for ribosome-inactivating protein gelonin (P33186) · a predicted model of the same protein · 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 P33186
- Elsewhere: RCSB PDB 3KU0 · PDBe 3KU0 · UniProt P33186
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