MolNFT v1 · #164981 · protein
Lsm protein (smap) from halobacterium salinarum
6TFL · RNA-binding protein lsm: “Lsm protein (smap) from halobacterium salinarum”. X-ray diffraction, 2 ligands (URI, CA), 2 pockets (best druggability 0.83). MolNFT v1 #164981 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6TFL
- Type
- protein
- Length
- 868 residues
- Chains
- 14
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA-binding protein lsm
- UniProt
- B0R5R2
- Ligands
- URI, CA
- Pockets
- 2 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 16% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M, N | RNA-binding protein lsm | protein | 62 | 16% helix, 47% strand | B0R5R2 |
Ligands and binding sites
- URI · Uridine · ligand · 14 copies · chains A, D, G, B, C, F, E, H, K, N, I, J, M, L
- CA · Calcium ion · metal · 28 copies · chains A, B, D, E, F, H, G, N, I, J, K, L, C, M
- GOL · Glycerol · additive · chains G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1084 | 0.83 | 0.84 | 147 | empty |
| 2 | 70 | 0.32 | 0.75 | 19 | URI |
Interfaces
35 interfaces between chains.
- B–C · 863 Ų buried · 12 hydrogen bonds · protein-protein
- I–N · 860 Ų buried · 16 hydrogen bonds · protein-protein
- C–F · 857 Ų buried · 16 hydrogen bonds · protein-protein
- B–G · 853 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 848 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6TFL · Lsm protein (SmAP) from Halobacterium salinarum · the same entry in another collection · 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 B0R5R2
- Elsewhere: RCSB PDB 6TFL · PDBe 6TFL · UniProt B0R5R2
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