Research workbench
Crystal structure of the S.POMBE SMC5/6 hinge domain
Analyse Crystal structure of the S.POMBE SMC5/6 hinge domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MG8
- Type
- protein
- Length
- 1,090 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Structural maintenance of chromosomes protein 5; Structural maintenance of chromosomes…
- UniProt
- O13710, P53692
- Ligands
- SO4
- Pockets
- 10 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 53% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Structural maintenance of chromosomes protein 5 | protein | 282 | 56% helix, 14% strand | O13710 |
| B | Structural maintenance of chromosomes protein 6 | protein | 264 | 48% helix, 13% strand | P53692 |
| C | Structural maintenance of chromosomes protein 5 | protein | 280 | 56% helix, 14% strand | O13710 |
| D | Structural maintenance of chromosomes protein 6 | protein | 264 | 51% helix, 13% strand | P53692 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 9 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1007 | 0.79 | 0.81 | 71 | empty |
| 2 | 711 | 0.75 | 0.80 | 67 | empty |
| 3 | 292 | 0.60 | 0.78 | 34 | empty |
| 4 | 317 | 0.57 | 0.76 | 38 | empty |
| 5 | 98 | 0.49 | 0.82 | 24 | empty |
Interfaces
3 interfaces between chains.
- C–D · 3266 Ų buried · 45 hydrogen bonds · protein-protein
- A–B · 3098 Ų buried · 40 hydrogen bonds · protein-protein
- B–D · 217 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5MG8 · Crystal structure of the S.pombe Smc5/6 hinge domain · the same entry in another collection · chain D against D, TM-score 1.00
- O13710 · AlphaFold monomer V2.0 prediction for structural maintenance of chromosomes protein 5… · a predicted model of the same protein · chain C against A, TM-score 0.84
- P53692 · AlphaFold monomer V2.0 prediction for structural maintenance of chromosomes protein 6… · a predicted model of the same protein · chain D against A, TM-score 0.77
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 O13710
- Every structure of UniProt P53692
- Elsewhere: RCSB PDB 5MG8 · PDBe 5MG8 · UniProt O13710 · UniProt P53692
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