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Cryo-EM structure of the centromeric nucleosome (native alpha satellite DNA) in complex with a single chain antibody fragment
Analyse Cryo-EM structure of the centromeric nucleosome (native alpha satellite DNA) in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6E0P
- Type
- protein + DNA
- Length
- 1,510 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3-like centromeric protein a; Histone H4; Histone H2A type 1-B/E; Histone H2B…
- UniProt
- P49450, P62805, P04908, P06899
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 10 distinct chains · 36% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Histone H3-like centromeric protein a | protein | 99 | 61% helix, 4% strand | P49450 |
| B, F | Histone H4 | protein | 80 | 61% helix, 9% strand | P62805 |
| C | Histone H2A type 1-B/E | protein | 107 | 56% helix, 7% strand | P04908 |
| D | Histone H2B type 1-J | protein | 95 | 73% helix, 4% strand | P06899 |
| G | Histone H2A type 1-B/E | protein | 108 | 56% helix, 6% strand | P04908 |
| H | Histone H2B type 1-J | protein | 94 | 72% helix, 4% strand | P06899 |
| I | DNA (145-mer) | dna | 145 | — | — |
| J | DNA (145-mer) | dna | 145 | — | — |
| M | Scfv | protein | 229 | 1% helix, 53% strand | — |
| N | Scfv | protein | 229 | 4% helix, 51% strand | — |
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 | 893 | 0.88 | 0.90 | 110 | empty |
| 2 | 710 | 0.72 | 0.79 | 58 | empty |
| 3 | 362 | 0.69 | 0.82 | 35 | empty |
| 4 | 425 | 0.68 | 0.80 | 42 | empty |
| 5 | 149 | 0.68 | 0.89 | 29 | empty |
Interfaces
42 interfaces between chains.
- I–J · 6304 Ų buried · 444 hydrogen bonds · nucleic-nucleic
- E–F · 2622 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 2615 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 2591 Ų buried · 20 hydrogen bonds · protein-protein
- G–H · 2569 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6E0P · Cryo-EM structure of the centromeric nucleosome (Native alpha satellite DNA) in complex… · the same entry in another collection · chain N against N, TM-score 1.00
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
- Elsewhere: RCSB PDB 6E0P · PDBe 6E0P · UniProt P49450 · UniProt P62805 · UniProt P04908 · UniProt P06899
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