Research workbench
Cryo-EM structure of cenp-a nucleosome in complex with kinetochore protein cenp-N
Analyse Cryo-EM structure of cenp-a nucleosome in complex with kinetochore protein… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BUZ
- Type
- protein + DNA
- Length
- 1,168 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; Histone H2B; DNA…
- UniProt
- P49450, P62805, P04908, P06899, P0AEY0, Q96H22
- Pockets
- 20 · best druggability 0.79
Structure
electron microscopy · 7 distinct chains · 55% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Histone H3-like centromeric protein a | protein | 91 | 66% helix, 3% strand | P49450 |
| B, F | Histone H4 | protein | 80 | 60% helix, 5% strand | P62805 |
| C, G | Histone H2A | protein | 107 | 53% helix, 5% strand | P04908 |
| D, H | Histone H2B | protein | 94 | 70% helix, 4% strand | P06899 |
| I | DNA (147-mer) | dna | 145 | — | — |
| J | DNA (147-mer) | dna | 145 | — | — |
| N | Maltose-binding periplasmic protein, centromere protein N chimera | protein | 134 | 37% helix, 0% strand | P0AEY0, Q96H22 |
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 | 542 | 0.79 | 0.86 | 63 | empty |
| 2 | 230 | 0.75 | 0.90 | 40 | empty |
| 3 | 239 | 0.75 | 0.89 | 45 | empty |
| 4 | 248 | 0.72 | 0.87 | 27 | empty |
| 5 | 487 | 0.70 | 0.81 | 48 | empty |
Interfaces
41 interfaces between chains.
- I–J · 6730 Ų buried · 856 hydrogen bonds · nucleic-nucleic
- G–H · 2572 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 2569 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 2542 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 2534 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 6BUZ · Cryo-EM structure of CENP-A nucleosome in complex with kinetochore protein CENP-N · the same entry in another collection · chain N against N, TM-score 1.00
- P49450 · AlphaFold monomer V2.0 prediction for histone H3-like centromeric protein a (P49450) · a predicted model of the same protein · chain E against A, TM-score 0.98
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 P04908
- Every structure of UniProt P06899
- Every structure of UniProt P0AEY0
- Every structure of UniProt Q96H22
- Elsewhere: RCSB PDB 6BUZ · PDBe 6BUZ · UniProt P49450 · UniProt P62805 · UniProt P04908 · UniProt P06899 · UniProt P0AEY0 · UniProt Q96H22
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