Research workbench
Nucleosome isolated from metaphase chromosome formed in xenopus egg extract (oligo fraction)
Analyse Nucleosome isolated from metaphase chromosome formed in xenopus egg extract… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KBE
- Type
- protein + DNA
- Length
- 1,072 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3.2; Histone H4; Histone H2A; Histone H2B 1.1; DNA (157-mer)
- UniProt
- P84233, P62799, Q6DKE3, P02281
- Pockets
- 20 · best druggability 0.77
Structure
electron microscopy · 9 distinct chains · 63% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone H3.2 | protein | 99 | 61% helix, 4% strand | P84233 |
| B | Histone H4 | protein | 81 | 60% helix, 9% strand | P62799 |
| C, G | Histone H2A | protein | 106 | 54% helix, 7% strand | Q6DKE3 |
| D | Histone H2B 1.1 | protein | 94 | 73% helix, 4% strand | P02281 |
| E | Histone H3.2 | protein | 97 | 64% helix, 4% strand | P84233 |
| F | Histone H4 | protein | 84 | 58% helix, 8% strand | P62799 |
| H | Histone H2B 1.1 | protein | 93 | 73% helix, 4% strand | P02281 |
| I | DNA (157-mer) | dna | 156 | — | — |
| J | DNA (157-mer) | dna | 156 | — | — |
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 | 845 | 0.77 | 0.80 | 68 | empty |
| 2 | 451 | 0.74 | 0.84 | 50 | empty |
| 3 | 566 | 0.72 | 0.80 | 53 | empty |
| 4 | 163 | 0.71 | 0.90 | 26 | empty |
| 5 | 178 | 0.68 | 0.88 | 26 | empty |
Interfaces
38 interfaces between chains.
- I–J · 6967 Ų buried · 554 hydrogen bonds · nucleic-nucleic
- E–F · 2763 Ų buried · 21 hydrogen bonds · protein-protein
- G–H · 2570 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 2535 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 2531 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 7KBE · Nucleosome isolated from metaphase chromosome formed in Xenopus egg extract (oligo… · the same entry in another collection · chain F against F, TM-score 1.00
- P84233 · AlphaFold monomer V2.0 prediction for histone H3.2 (P84233) · 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 P84233
- Every structure of UniProt P62799
- Every structure of UniProt Q6DKE3
- Every structure of UniProt P02281
- Elsewhere: RCSB PDB 7KBE · PDBe 7KBE · UniProt P84233 · UniProt P62799 · UniProt Q6DKE3 · UniProt P02281
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