Research workbench
Antibody and nucleosome complex
Analyse Antibody and nucleosome complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7K78
- Type
- protein + DNA
- Length
- 1,430 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CSE4; Histone H4; Histone H2A.1; Histone H2B.1; DNA (136-mer); Scfv
- UniProt
- P02309, P04911, P02293
- Pockets
- 20 · best druggability 0.73
Structure
electron microscopy · 11 distinct chains · 49% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CSE4 | protein | 95 | 68% helix, 4% strand | — |
| B | Histone H4 | protein | 79 | 62% helix, 9% strand | P02309 |
| C | Histone H2A.1 | protein | 101 | 55% helix, 7% strand | P04911 |
| D | Histone H2B.1 | protein | 94 | 74% helix, 4% strand | P02293 |
| E | CSE4 | protein | 98 | 66% helix, 4% strand | — |
| F | Histone H4 | protein | 80 | 61% helix, 9% strand | P02309 |
| G | Histone H2A.1 | protein | 100 | 49% helix, 7% strand | P04911 |
| H | Histone H2B.1 | protein | 93 | 75% helix, 4% strand | P02293 |
| I | DNA (136-mer) | dna | 116 | — | — |
| J | DNA (136-mer) | dna | 116 | — | — |
| K, L | Scfv | protein | 229 | 3% helix, 53% 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 | 487 | 0.73 | 0.83 | 51 | empty |
| 2 | 851 | 0.73 | 0.78 | 64 | empty |
| 3 | 424 | 0.72 | 0.83 | 48 | empty |
| 4 | 401 | 0.71 | 0.82 | 43 | empty |
| 5 | 471 | 0.69 | 0.80 | 37 | empty |
Interfaces
40 interfaces between chains.
- I–J · 4747 Ų buried · 264 hydrogen bonds · nucleic-nucleic
- E–F · 2686 Ų buried · 18 hydrogen bonds · protein-protein
- G–H · 2634 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 2630 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 2615 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7K78 · antibody and nucleosome complex · the same entry in another collection · chain L against L, 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 P02309
- Every structure of UniProt P04911
- Every structure of UniProt P02293
- Elsewhere: RCSB PDB 7K78 · PDBe 7K78 · UniProt P02309 · UniProt P04911 · UniProt P02293
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