Research workbench
Crystal structure of the bacillus subtilis smc head domain complexed with the cognate scpa C-terminal domain and soaked ATP
Analyse Crystal structure of the bacillus subtilis smc head domain complexed with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5H67
- Type
- protein
- Length
- 447 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chromosome partition protein smc; Segregation and condensation protein a
- UniProt
- P51834, P35154
- Ligands
- ATP
- Pockets
- 4 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chromosome partition protein smc | protein | 199 | 38% helix, 25% strand | P51834 |
| B | Chromosome partition protein smc | protein | 181 | 51% helix, 23% strand | P51834 |
| C | Segregation and condensation protein a | protein | 67 | 49% helix, 18% strand | P35154 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 248 | 0.61 | 0.80 | 31 | empty |
| 2 | 118 | 0.41 | 0.76 | 18 | empty |
| 3 | 88 | 0.36 | 0.75 | 17 | empty |
| 4 | 60 | 0.35 | 0.77 | 13 | empty |
Interfaces
3 interfaces between chains.
- A–B · 3526 Ų buried · 50 hydrogen bonds · protein-protein
- B–C · 981 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 274 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5H67 · Crystal structure of the Bacillus subtilis SMC head domain complexed with the cognate… · the same entry in another collection · chain A against A, TM-score 1.00
- P51834 · AlphaFold monomer V2.0 prediction for chromosome partition protein smc (P51834) · a predicted model of the same protein · chain B against A, TM-score 0.93
- P35154 · AlphaFold monomer V2.0 prediction for segregation and condensation protein a (P35154) · a predicted model of the same protein · chain C against A, TM-score 0.81
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 P51834
- Every structure of UniProt P35154
- Elsewhere: RCSB PDB 5H67 · PDBe 5H67 · UniProt P51834 · UniProt P35154
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