Research workbench
Structure of pyrococcus abyssii sm protein in complex with a uridine heptamer
Analyse Structure of pyrococcus abyssii sm protein in complex with a uridine heptamer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1M8V
- Type
- protein + RNA
- Length
- 1,036 residues
- Chains
- 21
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-R(P*UP*UP*UP*UP*UP*UP*U)-3'; Putative snrnp sm-like protein
- UniProt
- Q9V0Y8
- Ligands
- U, CA
- Pockets
- 15 · best druggability 0.58
Structure
x-ray diffraction · 4 distinct chains · 12% helix, 59% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| O, P, Q, R, S, U | 5'-R(P*UP*UP*UP*UP*UP*UP*U)-3' | rna | 6 | — | — |
| T | 5'-R(P*UP*UP*UP*UP*UP*UP*U)-3' | rna | 5 | — | — |
| A | Putative snrnp sm-like protein | protein | 72 | 14% helix, 58% strand | Q9V0Y8 |
| B, C, D, E, F, G, H, I, J, K, L, M, N | Putative snrnp sm-like protein | protein | 71 | 10% helix, 59% strand | Q9V0Y8 |
Ligands and binding sites
- U · Uridine-5'-monophosphate · ligand · 14 copies · chains A, B, G, C, D, E, F, H, I, N, J, K, L, M
- CA · Calcium ion · metal · 7 copies · chains O, P, Q, R, S, T, U
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 401 | 0.58 | 0.75 | 46 | U |
| 2 | 350 | 0.55 | 0.75 | 49 | U |
| 3 | 259 | 0.51 | 0.75 | 20 | empty |
| 4 | 257 | 0.49 | 0.74 | 29 | U |
| 5 | 229 | 0.48 | 0.75 | 26 | U |
Interfaces
48 interfaces between chains.
- A–B · 854 Ų buried · 14 hydrogen bonds · protein-protein
- L–M · 828 Ų buried · 17 hydrogen bonds · protein-protein
- E–F · 815 Ų buried · 14 hydrogen bonds · protein-protein
- J–K · 810 Ų buried · 15 hydrogen bonds · protein-protein
- I–J · 805 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 1M8V · Structure of Pyrococcus abyssii Sm Protein in Complex with a Uridine Heptamer · the same entry in another collection · chain L against L, 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 Q9V0Y8
- Elsewhere: RCSB PDB 1M8V · PDBe 1M8V · UniProt Q9V0Y8
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