Research workbench
Cohesin complex with loader gripping DNA
Analyse Cohesin complex with loader gripping DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YUF
- Type
- protein + DNA
- Length
- 2,328 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cohesin subunit RAD21; Sister chromatid cohesion protein MIS4; Structural maintenance of…
- UniProt
- P30776, Q09725, O94383, O42649
- Ligands
- BEF, ADP
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 6 distinct chains · 56% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Cohesin subunit RAD21 | protein | 152 | 55% helix, 3% strand | P30776 |
| D | Sister chromatid cohesion protein MIS4 | protein | 1272 | 62% helix, 1% strand | Q09725 |
| A | Structural maintenance of chromosomes protein 1 | protein | 384 | 42% helix, 18% strand | O94383 |
| C | Structural maintenance of chromosomes protein 3 | protein | 456 | 50% helix, 13% strand | O42649 |
| X | DNA (32-mer) | dna | 32 | — | — |
| Y | DNA (32-mer) | dna | 32 | — | — |
Ligands and binding sites
- BEF · Beryllium trifluoride ion · ligand · 2 copies · chains A, C
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 778 | 0.82 | 0.85 | 84 | BEF, ADP |
| 2 | 303 | 0.80 | 0.91 | 52 | empty |
| 3 | 1009 | 0.78 | 0.80 | 107 | empty |
| 4 | 963 | 0.76 | 0.78 | 98 | empty |
| 5 | 83 | 0.75 | 0.96 | 18 | empty |
Interfaces
14 interfaces between chains.
- B–C · 2370 Ų buried · 17 hydrogen bonds · protein-protein
- X–Y · 1473 Ų buried · 103 hydrogen bonds · nucleic-nucleic
- D–A · 1342 Ų buried · 17 hydrogen bonds · protein-protein
- D–C · 1160 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 1097 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6YUF · Cohesin complex with loader gripping DNA · the same entry in another collection · chain Y against Y, TM-score 1.00
- O94383 · AlphaFold monomer V2.0 prediction for structural maintenance of chromosomes protein 1… · a predicted model of the same protein · chain A against A, TM-score 0.94
- Q09725 · AlphaFold monomer V2.0 prediction for sister chromatid cohesion protein MIS4 (Q09725) · a predicted model of the same protein · chain D against A, TM-score 0.86
- O42649 · 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 0.75
- P30776 · AlphaFold monomer V2.0 prediction for cohesin subunit RAD21 (P30776) · a predicted model of the same protein · chain B against A, TM-score 0.50
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 P30776
- Every structure of UniProt Q09725
- Every structure of UniProt O94383
- Every structure of UniProt O42649
- Elsewhere: RCSB PDB 6YUF · PDBe 6YUF · UniProt P30776 · UniProt Q09725 · UniProt O94383 · UniProt O42649
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