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Crystal structure of an sm-like protein (af-SM1) from archaeoglobus fulgidus complexed with short poly-U RNA
Analyse Crystal structure of an sm-like protein (af-SM1) from archaeoglobus fulgidus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1I5L
- Type
- protein + RNA
- Length
- 1,016 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-R(*UP*UP*U)-3'; Putative snrnp sm-like protein af-SM1
- UniProt
- O29386
- Ligands
- URI
- Pockets
- 13 · best druggability 0.75
Structure
x-ray diffraction · 8 distinct chains · 12% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| U, Y | 5'-R(*UP*UP*U)-3' | rna | 3 | — | — |
| A, E, N | Putative snrnp sm-like protein af-SM1 | protein | 71 | 13% helix, 59% strand | O29386 |
| B | Putative snrnp sm-like protein af-SM1 | protein | 73 | 12% helix, 55% strand | O29386 |
| C | Putative snrnp sm-like protein af-SM1 | protein | 74 | 12% helix, 57% strand | O29386 |
| D | Putative snrnp sm-like protein af-SM1 | protein | 73 | 12% helix, 58% strand | O29386 |
| F, G, H, J, K, L | Putative snrnp sm-like protein af-SM1 | protein | 72 | 13% helix, 53% strand | O29386 |
| I | Putative snrnp sm-like protein af-SM1 | protein | 73 | 12% helix, 58% strand | O29386 |
| M | Putative snrnp sm-like protein af-SM1 | protein | 72 | 13% helix, 53% strand | O29386 |
Ligands and binding sites
- URI · Uridine · ligand · 4 copies · chains U, A, B, G, C, H, I, N
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1151 | 0.75 | 0.78 | 121 | URI |
| 2 | 391 | 0.55 | 0.74 | 39 | URI |
| 3 | 89 | 0.41 | 0.78 | 20 | empty |
| 4 | 84 | 0.40 | 0.78 | 15 | empty |
| 5 | 112 | 0.39 | 0.75 | 23 | empty |
Interfaces
31 interfaces between chains.
- C–D · 953 Ų buried · 9 hydrogen bonds · protein-protein
- I–J · 938 Ų buried · 8 hydrogen bonds · protein-protein
- M–N · 922 Ų buried · 9 hydrogen bonds · protein-protein
- L–M · 887 Ų buried · 8 hydrogen bonds · protein-protein
- F–G · 882 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 1I5L · Crystal structure of an sm-like protein (af-SM1) from archaeoglobus fulgidus complexed… · the same entry in another collection · chain N against N, 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 O29386
- Elsewhere: RCSB PDB 1I5L · PDBe 1I5L · UniProt O29386
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