Research workbench
Cryo-EM structure of human cohesin-nipbl-DNA complex
Analyse Cryo-EM structure of human cohesin-nipbl-DNA complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WG3
- Type
- protein + DNA
- Length
- 3,762 residues
- Chains
- 7
- 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, Q8WVM7, Q6KC79
- Ligands
- ANP
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 7 distinct chains · 62% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Structural maintenance of chromosomes protein 1A | protein | 561 | 44% helix, 19% strand | Q14683 |
| B | Structural maintenance of chromosomes protein 3 | protein | 693 | 52% helix, 14% strand | Q9UQE7 |
| C | Double-strand-break repair protein RAD21 homolog | protein | 248 | 50% helix, 5% strand | O60216 |
| D | Cohesin subunit sa-1 | protein | 932 | 72% helix, 0% strand | Q8WVM7 |
| E | Nipped-B-like protein | protein | 1226 | 71% helix, 0% strand | Q6KC79 |
| F | DNA (51-mer) | dna | 51 | — | — |
| G | DNA (51-mer) | dna | 51 | — | — |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 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 | 872 | 0.86 | 0.88 | 119 | ANP |
| 2 | 905 | 0.80 | 0.82 | 82 | empty |
| 3 | 174 | 0.80 | 0.94 | 32 | empty |
| 4 | 534 | 0.80 | 0.86 | 84 | empty |
| 5 | 358 | 0.79 | 0.89 | 47 | ANP |
Interfaces
20 interfaces between chains.
- C–D · 2949 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 2353 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 2207 Ų buried · 15 hydrogen bonds · protein-protein
- F–G · 2080 Ų buried · 146 hydrogen bonds · nucleic-nucleic
- B–E · 1917 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6WG3 · Cryo-EM structure of human Cohesin-NIPBL-DNA complex · the same entry in another collection · chain G against G, TM-score 1.00
- Q8WVM7 · AlphaFold monomer V2.0 prediction for cohesin subunit sa-1 (Q8WVM7) · a predicted model of the same protein · chain D against A, TM-score 0.93
- 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 0.69
- 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 0.52
- 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 0.32
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 Q8WVM7
- Every structure of UniProt Q6KC79
- Elsewhere: RCSB PDB 6WG3 · PDBe 6WG3 · UniProt Q14683 · UniProt Q9UQE7 · UniProt O60216 · UniProt Q8WVM7 · UniProt Q6KC79
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