Research workbench
Cryo-EM structure of human kinetochore protein cenp-N with the centromeric nucleosome containing cenp-a
Analyse Cryo-EM structure of human kinetochore protein cenp-N with the centromeric… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6C0W
- Type
- protein + DNA
- Length
- 1,203 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; 147 mer DNA…
- UniProt
- P49450, P62805, Q93077, P62807, Q96H22
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 10 distinct chains · 55% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone H3-like centromeric protein a | protein | 89 | 53% helix, 4% strand | P49450 |
| B | Histone H4 | protein | 79 | 58% helix, 8% strand | P62805 |
| C | Histone H2A | protein | 99 | 57% helix, 4% strand | Q93077 |
| D, H | Histone H2B | protein | 92 | 66% helix, 2% strand | P62807 |
| E | Histone H3-like centromeric protein a | protein | 91 | 64% helix, 3% strand | P49450 |
| F | Histone H4 | protein | 78 | 60% helix, 6% strand | P62805 |
| G | Histone H2A | protein | 100 | 53% helix, 6% strand | Q93077 |
| I | 147 mer DNA | dna | 139 | — | — |
| J | 147 mer DNA | dna | 139 | — | — |
| K | Centromere protein N | protein | 205 | 43% helix, 19% strand | 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 | 772 | 0.84 | 0.87 | 82 | empty |
| 2 | 1000 | 0.82 | 0.83 | 96 | empty |
| 3 | 356 | 0.76 | 0.87 | 46 | empty |
| 4 | 333 | 0.74 | 0.86 | 48 | empty |
| 5 | 366 | 0.73 | 0.85 | 37 | empty |
Interfaces
42 interfaces between chains.
- I–J · 6346 Ų buried · 527 hydrogen bonds · nucleic-nucleic
- C–D · 2540 Ų buried · 21 hydrogen bonds · protein-protein
- E–F · 2515 Ų buried · 11 hydrogen bonds · protein-protein
- G–H · 2509 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 2494 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6C0W · Cryo-EM structure of human kinetochore protein CENP-N with the centromeric nucleosome… · the same entry in another collection · chain K against K, 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 A against A, TM-score 0.97
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 Q93077
- Every structure of UniProt P62807
- Every structure of UniProt Q96H22
- Elsewhere: RCSB PDB 6C0W · PDBe 6C0W · UniProt P49450 · UniProt P62805 · UniProt Q93077 · UniProt P62807 · UniProt Q96H22
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