Research workbench
Cryo-EM structure of S.CEREVISIAE cohesin-SCC2-DNA complex
Analyse Cryo-EM structure of S.CEREVISIAE cohesin-SCC2-DNA complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZZ6
- Type
- protein + DNA
- Length
- 1,984 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Structural maintenance of chromosomes protein 1,STRUCTURAL maintenance of chromosomes…
- UniProt
- P32908, P47037, Q12158, Q04002
- Ligands
- ATP, MG
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · 6 distinct chains · 61% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Structural maintenance of chromosomes protein 1,STRUCTURAL maintenance of chromosomes protein 1,STRUCTURAL maintenance of chromosomes protein 1 | protein | 360 | 36% helix, 23% strand | P32908 |
| B | Structural maintenance of chromosomes protein 3,STRUCTURAL maintenance of chromosomes protein 3,STRUCTURAL maintenance of chromosomes protein 3 | protein | 423 | 48% helix, 15% strand | P47037 |
| C | Sister chromatid cohesion protein 1,SISTER chromatid cohesion protein 1,SISTER chromatid cohesion protein 1 | protein | 83 | 67% helix, 11% strand | Q12158 |
| D | Sister chromatid cohesion protein 2 | protein | 1050 | 74% helix, 1% strand | Q04002 |
| F | DNA (34-mer) | dna | 34 | — | — |
| G | DNA (34-mer) | dna | 34 | — | — |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 902 | 0.80 | 0.83 | 93 | empty |
| 2 | 987 | 0.78 | 0.80 | 101 | empty |
| 3 | 495 | 0.77 | 0.84 | 62 | empty |
| 4 | 150 | 0.76 | 0.94 | 33 | ATP |
| 5 | 405 | 0.75 | 0.85 | 54 | ATP, MG |
Interfaces
13 interfaces between chains.
- B–C · 1714 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1527 Ų buried · 19 hydrogen bonds · protein-protein
- F–G · 1433 Ų buried · 79 hydrogen bonds · nucleic-nucleic
- B–D · 1214 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 1162 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6ZZ6 · Cryo-EM structure of S.cerevisiae cohesin-Scc2-DNA complex · the same entry in another collection · chain G against G, TM-score 1.00
- P32908 · 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 0.98
- Q04002 · AlphaFold monomer V2.0 prediction for sister chromatid cohesion protein 2 (Q04002) · a predicted model of the same protein · chain D against A, TM-score 0.93
- P47037 · AlphaFold monomer V2.0 prediction for structural maintenance of chromosomes protein 3… · a predicted model of the same protein · chain B against A, TM-score 0.83
- Q12158 · AlphaFold monomer V2.0 prediction for sister chromatid cohesion protein 1 (Q12158) · a predicted model of the same protein · chain C against A, TM-score 0.43
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 P32908
- Every structure of UniProt P47037
- Every structure of UniProt Q12158
- Every structure of UniProt Q04002
- Elsewhere: RCSB PDB 6ZZ6 · PDBe 6ZZ6 · UniProt P32908 · UniProt P47037 · UniProt Q12158 · UniProt Q04002
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