Research workbench
Crystal structure of an engaged dimer of the geobacillus stearothermophilus smc head domain
Analyse Crystal structure of an engaged dimer of the geobacillus stearothermophilus smc… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5H68
- Type
- protein
- Length
- 657 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chromosome partition protein smc
- UniProt
- A0A0K2H586
- Ligands
- AGS, MG
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chromosome partition protein smc | protein | 325 | 33% helix, 25% strand | A0A0K2H586 |
| B | Chromosome partition protein smc | protein | 332 | 34% helix, 24% strand | A0A0K2H586 |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 169 | 0.80 | 0.96 | 39 | AGS, MG |
| 2 | 133 | 0.77 | 0.96 | 38 | AGS, MG |
| 3 | 695 | 0.72 | 0.79 | 66 | empty |
| 4 | 167 | 0.50 | 0.78 | 30 | empty |
| 5 | 162 | 0.48 | 0.77 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 1739 Ų buried · 45 hydrogen bonds · protein-protein
Compared structures
- 5H68 · Crystal structure of an engaged dimer of the Geobacillus stearothermophilus SMC head… · 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 A0A0K2H586
- Elsewhere: RCSB PDB 5H68 · PDBe 5H68 · UniProt A0A0K2H586
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