Research workbench
Crystal structure of the atpgs-engaged smc head domain with an extended coiled coil bound to the C-terminal domain of scpa derived from bacillus subtilis
Analyse Crystal structure of the atpgs-engaged smc head domain with an extended coiled… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XG3
- Type
- protein
- Length
- 866 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chromosome partition protein smc; Segregation and condensation protein a
- UniProt
- P51834, A0A1N6WAJ8
- Ligands
- AGS, MG, CO
- Pockets
- 18 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chromosome partition protein smc | protein | 371 | 42% helix, 20% strand | P51834 |
| B | Chromosome partition protein smc | protein | 374 | 39% helix, 21% strand | P51834 |
| C | Segregation and condensation protein a | protein | 68 | 40% helix, 12% strand | A0A1N6WAJ8 |
| D | Segregation and condensation protein a | protein | 53 | 49% helix, 9% strand | A0A1N6WAJ8 |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- CO · Cobalt (II) ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 548 | 0.80 | 0.86 | 67 | AGS, MG |
| 2 | 478 | 0.74 | 0.83 | 71 | empty |
| 3 | 237 | 0.71 | 0.86 | 44 | empty |
| 4 | 54 | 0.70 | 0.97 | 17 | empty |
| 5 | 51 | 0.70 | 0.97 | 22 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1008 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 841 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 630 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 217 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 60 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5XG3 · Crystal structure of the ATPgS-engaged Smc head domain with an extended coiled coil bound… · 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 A against A, TM-score 0.89
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 A0A1N6WAJ8
- Elsewhere: RCSB PDB 5XG3 · PDBe 5XG3 · UniProt P51834 · UniProt A0A1N6WAJ8
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