Research workbench
Crystal structure of M-crystallin in the presence of nickel
Analyse Crystal structure of M-crystallin in the presence of nickel in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HT9
- Type
- protein
- Length
- 168 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.869
- Source
- Methanosarcina acetivorans C2A
- Molecule
- Beta/gama crystallin family protein
- UniProt
- Q8TMX3
- Ligands
- MG, NI
- Pockets
- 1 · best druggability 0.39
Structure
x-ray diffraction · resolution 1.869 · 1 distinct chain · 11% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta/gama crystallin family protein | protein | 84 | 11% helix, 49% strand | Q8TMX3 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, B
- NI · Nickel (II) ion · metal · 2 copies · chains A, B
- BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 63 | 0.39 | 0.79 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 335 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5HT9 · Crystal structure of M-crystallin in the presence of nickel · 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 Q8TMX3
- Elsewhere: RCSB PDB 5HT9 · PDBe 5HT9 · UniProt Q8TMX3
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