Research workbench
CLASS2C : cenp-a nucleosome in complex with cenp-C central region
Analyse CLASS2C : cenp-a nucleosome in complex with cenp-C central region in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SEF
- Type
- protein + DNA
- Length
- 1,041 residues
- Chains
- 11
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3-like centromeric protein a; Histone H4; Histone H2A type 2-a; Histone H2B type…
- UniProt
- P49450, P62805, Q6FI13, P62807, Q03188
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 10 distinct chains · 61% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Histone H3-like centromeric protein a | protein | 98 | 65% helix, 4% strand | P49450 |
| B | Histone H4 | protein | 78 | 60% helix, 6% strand | P62805 |
| C | Histone H2A type 2-a | protein | 96 | 54% helix, 7% strand | Q6FI13 |
| D | Histone H2B type 1-C/E/F/G/I | protein | 92 | 74% helix, 4% strand | P62807 |
| F | Histone H4 | protein | 78 | 63% helix, 9% strand | P62805 |
| G | Histone H2A type 2-a | protein | 103 | 51% helix, 5% strand | Q6FI13 |
| H | Histone H2B type 1-C/E/F/G/I | protein | 90 | 74% helix, 4% strand | P62807 |
| I | DNA (145-mer) | dna | 145 | — | — |
| J | DNA (145-mer) | dna | 145 | — | — |
| V | Centromere protein C | protein | 18 | 0% helix, 0% strand | Q03188 |
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 | 365 | 0.81 | 0.90 | 48 | empty |
| 2 | 102 | 0.70 | 0.93 | 25 | empty |
| 3 | 859 | 0.70 | 0.76 | 51 | empty |
| 4 | 854 | 0.69 | 0.75 | 52 | empty |
| 5 | 78 | 0.65 | 0.92 | 25 | empty |
Interfaces
43 interfaces between chains.
- I–J · 6573 Ų buried · 557 hydrogen bonds · nucleic-nucleic
- A–B · 2601 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 2593 Ų buried · 23 hydrogen bonds · protein-protein
- G–H · 2544 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 2460 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
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 P49450
- Every structure of UniProt P62805
- Every structure of UniProt Q6FI13
- Every structure of UniProt P62807
- Every structure of UniProt Q03188
- Elsewhere: RCSB PDB 6SEF · PDBe 6SEF · UniProt P49450 · UniProt P62805 · UniProt Q6FI13 · UniProt P62807 · UniProt Q03188
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