MolNFT v1 · #158683 · protein + DNA
Cryo-EM structure of the centromeric nucleosome with native alpha satellite DNA
6O1D · Histone H3-like centromeric protein a: “Cryo-EM structure of the centromeric nucleosome with native alpha satellite DNA”. Electron microscopy, 20 pockets (best druggability 0.85). MolNFT v1 #158683 on GenesisL1: 3D structure…
- PDB
- 6O1D
- Type
- protein + DNA
- Length
- 1,051 residues
- Chains
- 10
- 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 0.85
Structure
electron microscopy · 7 distinct chains · 55% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Histone H3-like centromeric protein a | protein | 99 | 51% helix, 4% strand | P49450 |
| B, F | Histone H4 | protein | 80 | 64% helix, 9% strand | P62805 |
| C | Histone H2A type 1-B/E | protein | 107 | 50% helix, 7% strand | P04908 |
| D, H | Histone H2B type 1-J | protein | 94 | 72% helix, 4% strand | P06899 |
| G | Histone H2A type 1-B/E | protein | 108 | 44% helix, 6% strand | P04908 |
| I | DNA (145-mer) | dna | 145 | — | — |
| J | DNA (145-mer) | dna | 145 | — | — |
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 878 | 0.85 | 0.87 | 110 | empty |
| 2 | 597 | 0.83 | 0.88 | 67 | empty |
| 3 | 174 | 0.69 | 0.88 | 28 | empty |
| 4 | 176 | 0.67 | 0.87 | 31 | empty |
| 5 | 418 | 0.64 | 0.78 | 34 | empty |
Interfaces
36 interfaces between chains.
- I–J · 6272 Ų buried · 410 hydrogen bonds · nucleic-nucleic
- E–F · 2641 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 2618 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 2560 Ų buried · 14 hydrogen bonds · protein-protein
- G–H · 2550 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 6O1D · Cryo-EM structure of the centromeric nucleosome with native alpha satellite DNA · the same entry in another collection · chain J against J, 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 0.96
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 6O1D · PDBe 6O1D · UniProt P49450 · UniProt P62805 · UniProt P04908 · UniProt P06899
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