Research workbench
Structure of mutant rip from barley seeds in complex with AMP
Analyse Structure of mutant rip from barley seeds in complex with AMP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4FBC
- Type
- protein
- Length
- 1,112 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein synthesis inhibitor I
- EC
- 3.2.2.22
- UniProt
- P22244
- Ligands
- AMP
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Protein synthesis inhibitor I (EC 3.2.2.22) | protein | 278 | 40% helix, 16% strand | P22244 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 971 | 0.73 | 0.76 | 66 | empty |
| 2 | 938 | 0.73 | 0.77 | 68 | empty |
| 3 | 332 | 0.64 | 0.80 | 42 | empty |
| 4 | 262 | 0.60 | 0.80 | 39 | empty |
| 5 | 166 | 0.52 | 0.79 | 27 | AMP |
Interfaces
5 interfaces between chains.
- A–B · 756 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 672 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 441 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 434 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 34 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4FBC · Structure of mutant RIP from barley seeds in complex with AMP · the same entry in another collection · chain A against A, TM-score 1.00
- P22244 · AlphaFold monomer V2.0 prediction for protein synthesis inhibitor I (P22244) · a predicted model of the same protein · chain A 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 P22244
- Elsewhere: RCSB PDB 4FBC · PDBe 4FBC · UniProt P22244
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