Research workbench
Cryo-EM structure of human cohesin-nipbl-DNA complex without STAG1
Analyse Cryo-EM structure of human cohesin-nipbl-DNA complex without STAG1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WGE
- Type
- protein + DNA
- Length
- 2,366 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Structural maintenance of chromosomes protein 1A; Structural maintenance of chromosomes…
- UniProt
- Q14683, Q9UQE7, O60216, Q6KC79
- Ligands
- ANP, MG
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 6 distinct chains · 61% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Structural maintenance of chromosomes protein 1A | protein | 390 | 44% helix, 20% strand | Q14683 |
| B | Structural maintenance of chromosomes protein 3 | protein | 490 | 51% helix, 14% strand | Q9UQE7 |
| C | Double-strand-break repair protein RAD21 homolog | protein | 174 | 51% helix, 7% strand | O60216 |
| E | Nipped-B-like protein | protein | 1226 | 71% helix, 0% strand | Q6KC79 |
| F | DNA (43-mer) | dna | 43 | — | — |
| G | DNA (43-mer) | dna | 43 | — | — |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 779 | 0.85 | 0.88 | 102 | ANP, MG |
| 2 | 151 | 0.77 | 0.94 | 26 | ANP |
| 3 | 378 | 0.76 | 0.87 | 71 | empty |
| 4 | 716 | 0.76 | 0.82 | 52 | empty |
| 5 | 123 | 0.72 | 0.92 | 19 | empty |
Interfaces
13 interfaces between chains.
- B–C · 2479 Ų buried · 11 hydrogen bonds · protein-protein
- B–E · 2045 Ų buried · 14 hydrogen bonds · protein-protein
- F–G · 1768 Ų buried · 110 hydrogen bonds · nucleic-nucleic
- A–B · 1609 Ų buried · 18 hydrogen bonds · protein-protein
- A–E · 1515 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6WGE · Cryo-EM structure of human Cohesin-NIPBL-DNA complex without STAG1 · the same entry in another collection · chain G against G, TM-score 1.00
- Q14683 · AlphaFold monomer V2.0 prediction for structural maintenance of chromosomes protein 1A… · a predicted model of the same protein · chain A against A, TM-score 0.98
- Q9UQE7 · 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 0.73
- O60216 · AlphaFold monomer V2.0 prediction for double-strand-break repair protein RAD21 homolog… · a predicted model of the same protein · chain C against A, TM-score 0.45
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 Q14683
- Every structure of UniProt Q9UQE7
- Every structure of UniProt O60216
- Every structure of UniProt Q6KC79
- Elsewhere: RCSB PDB 6WGE · PDBe 6WGE · UniProt Q14683 · UniProt Q9UQE7 · UniProt O60216 · UniProt Q6KC79
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