Research workbench
Crystal structure of a complex of the archaeal ribosomal stalk protein AP1 and the GDP-bound archaeal elongation factor AEF1ALPHA
Analyse Crystal structure of a complex of the archaeal ribosomal stalk protein AP1 and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WY9
- Type
- protein
- Length
- 884 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Elongation factor 1-alpha; 50S ribosomal protein L12
- UniProt
- O59153, O57705
- Ligands
- GDP
- Pockets
- 10 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Elongation factor 1-alpha | protein | 416 | 23% helix, 35% strand | O59153 |
| C, D | 50S ribosomal protein L12 | protein | 26 | 88% helix, 0% strand | O57705 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 482 | 0.69 | 0.79 | 55 | GDP |
| 2 | 370 | 0.65 | 0.79 | 52 | GDP |
| 3 | 201 | 0.60 | 0.81 | 27 | empty |
| 4 | 195 | 0.56 | 0.79 | 24 | empty |
| 5 | 174 | 0.54 | 0.79 | 23 | empty |
Interfaces
6 interfaces between chains.
- A–C · 586 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 551 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 456 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 414 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 313 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3WY9 · Crystal structure of a complex of the archaeal ribosomal stalk protein aP1 and the… · the same entry in another collection · chain A against A, TM-score 1.00
- O57705 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L12 (O57705) · a predicted model of the same protein · chain C against A, TM-score 0.85
- O59153 · AlphaFold monomer V2.0 prediction for elongation factor 1-alpha (O59153) · a predicted model of the same protein · chain B against A, TM-score 0.55
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 O59153
- Every structure of UniProt O57705
- Elsewhere: RCSB PDB 3WY9 · PDBe 3WY9 · UniProt O59153 · UniProt O57705
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