Research workbench
The structure of the centromeric nucleosome containing cenp-a
Analyse The structure of the centromeric nucleosome containing cenp-a in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3AN2
- Type
- protein + DNA
- Length
- 948 residues
- Chains
- 10
- Method
- x-ray diffraction
- 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, B2R4R0, P04908, P06899
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 8 distinct chains · 55% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone H3-like centromeric protein a | protein | 89 | 48% helix, 4% strand | P49450 |
| B | Histone H4 | protein | 78 | 59% helix, 8% strand | B2R4R0 |
| C | Histone H2A type 1-B/E | protein | 97 | 55% helix, 4% strand | P04908 |
| D, H | Histone H2B type 1-J | protein | 90 | 62% helix, 3% strand | P06899 |
| E | Histone H3-like centromeric protein a | protein | 83 | 48% helix, 4% strand | P49450 |
| F | Histone H4 | protein | 79 | 59% helix, 5% strand | B2R4R0 |
| G | Histone H2A type 1-B/E | protein | 100 | 51% helix, 6% strand | P04908 |
| I, J | 147 mer DNA | dna | 121 | — | — |
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 | 472 | 0.78 | 0.86 | 59 | empty |
| 2 | 346 | 0.75 | 0.86 | 43 | empty |
| 3 | 226 | 0.73 | 0.88 | 41 | empty |
| 4 | 685 | 0.66 | 0.75 | 52 | empty |
| 5 | 143 | 0.64 | 0.86 | 26 | empty |
Interfaces
38 interfaces between chains.
- I–J · 5662 Ų buried · 483 hydrogen bonds · nucleic-nucleic
- C–D · 2588 Ų buried · 23 hydrogen bonds · protein-protein
- G–H · 2564 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 2460 Ų buried · 23 hydrogen bonds · protein-protein
- E–F · 2433 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (engineered).
Compared structures
- 3AN2 · The structure of the centromeric nucleosome containing CENP-A · the same entry in another collection · chain F against F, TM-score 1.00
- P06899 · AlphaFold monomer V2.0 prediction for histone H2B type 1-J (P06899) · a predicted model of the same protein · chain D against A, TM-score 0.97
- 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 0.96
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 B2R4R0
- Every structure of UniProt P04908
- Every structure of UniProt P06899
- Elsewhere: RCSB PDB 3AN2 · PDBe 3AN2 · UniProt P49450 · UniProt B2R4R0 · UniProt P04908 · UniProt P06899
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