Research workbench
Crystal structure of the P.AEROPHILUM SMAP1 heptamer in a new crystal form (C2221)
Analyse Crystal structure of the P.AEROPHILUM SMAP1 heptamer in a new crystal form… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1LNX
- Type
- protein
- Length
- 513 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Small nuclear ribonucleoprotein homolog (sm-like)
- UniProt
- Q8ZYG5
- Ligands
- URI
- Pockets
- 9 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | Small nuclear ribonucleoprotein homolog (sm-like) | protein | 74 | 15% helix, 57% strand | Q8ZYG5 |
| B, C, D, E, G | Small nuclear ribonucleoprotein homolog (sm-like) | protein | 73 | 18% helix, 58% strand | Q8ZYG5 |
Ligands and binding sites
- URI · Uridine · ligand · 7 copies · chains A, B, C, D, E, F, G
- GOL · Glycerol · additive · 10 copies · chains A, B, C, D, E, F, G
- ACY · Acetic acid · additive · 2 copies · chains A, B, C, D, E, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 286 | 0.58 | 0.79 | 29 | ACY |
| 2 | 219 | 0.48 | 0.75 | 62 | GOL |
| 3 | 86 | 0.39 | 0.77 | 16 | URI |
| 4 | 72 | 0.37 | 0.77 | 18 | URI |
| 5 | 73 | 0.35 | 0.76 | 18 | URI |
Interfaces
14 interfaces between chains.
- C–D · 924 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 922 Ų buried · 18 hydrogen bonds · protein-protein
- E–F · 920 Ų buried · 19 hydrogen bonds · protein-protein
- A–G · 919 Ų buried · 19 hydrogen bonds · protein-protein
- D–E · 910 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 1LNX · Crystal structure of the P.aerophilum SmAP1 heptamer in a new crystal form (C2221) · 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 Q8ZYG5
- Elsewhere: RCSB PDB 1LNX · PDBe 1LNX · UniProt Q8ZYG5
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.