MolNFT v1 · #161813 · protein
Structural basis of cohesin ring opening
6QPW · Structural maintenance of chromosomes PROTEIN,STRUCTURAL…: “Structural basis of cohesin ring opening”. Electron microscopy, 2 ligands (AGS, MG), 5 pockets (best druggability 0.87). MolNFT v1 #161813 on GenesisL1: 3D structure…
- PDB
- 6QPW
- Type
- protein
- Length
- 839 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Structural maintenance of chromosomes PROTEIN,STRUCTURAL maintenance of chromosomes…
- UniProt
- G0SGH3, Q12158, P47037
- Ligands
- AGS, MG
- Pockets
- 5 · best druggability 0.87
Structure
electron microscopy · 4 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Structural maintenance of chromosomes PROTEIN,STRUCTURAL maintenance of chromosomes protein | protein | 183 | 38% helix, 23% strand | G0SGH3 |
| B | Sister chromatid cohesion protein 1 | protein | 81 | 58% helix, 15% strand | Q12158 |
| C | Structural maintenance of chromosomes protein 3,STRUCTURAL maintenance of chromosomes protein 3 | protein | 377 | 39% helix, 13% strand | P47037 |
| E | Sister chromatid cohesion protein 1,STRUCTURAL maintenance of chromosomes protein | protein | 198 | 48% helix, 20% strand | G0SGH3, Q12158 |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 2 copies · chains A, C, E
- MG · Magnesium ion · metal · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1185 | 0.87 | 0.88 | 138 | MG, AGS |
| 2 | 222 | 0.66 | 0.84 | 27 | empty |
| 3 | 86 | 0.43 | 0.79 | 19 | empty |
| 4 | 52 | 0.43 | 0.83 | 12 | empty |
| 5 | 83 | 0.38 | 0.77 | 18 | empty |
Interfaces
6 interfaces between chains.
- A–E · 3654 Ų buried · 41 hydrogen bonds · protein-protein
- B–E · 1110 Ų buried · 11 hydrogen bonds · protein-protein
- C–E · 794 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 408 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 263 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 disulfide (covalent ligand, disulfide).
Compared structures
- 6QPW · Structural basis of cohesin ring opening · the same entry in another collection · chain A against A, TM-score 1.00
- Q12158 · AlphaFold monomer V2.0 prediction for sister chromatid cohesion protein 1 (Q12158) · a predicted model of the same protein · chain B against A, TM-score 0.96
- P47037 · AlphaFold monomer V2.0 prediction for structural maintenance of chromosomes protein 3… · a predicted model of the same protein · chain C against A, TM-score 0.85
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 G0SGH3
- Every structure of UniProt Q12158
- Every structure of UniProt P47037
- Elsewhere: RCSB PDB 6QPW · PDBe 6QPW · UniProt G0SGH3 · UniProt Q12158 · UniProt P47037
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