Research workbench
Structural mechanism of nucleosome dynamics governed by human histone variants H2A.B and H2A.Z.2.2
Analyse Structural mechanism of nucleosome dynamics governed by human histone variants… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6M4D
- Type
- protein + DNA
- Length
- 932 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3.1; Histone H4; Histone H2A.V; Histone H2B type 2-E; DNA (125-mer)
- UniProt
- P68431, P62805, Q71UI9, Q16778
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 6 distinct chains · 66% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Histone H3.1 | protein | 77 | 68% helix, 5% strand | P68431 |
| B, F | Histone H4 | protein | 80 | 60% helix, 6% strand | P62805 |
| C, G | Histone H2A.V | protein | 91 | 60% helix, 2% strand | Q71UI9 |
| D, H | Histone H2B type 2-E | protein | 93 | 74% helix, 1% strand | Q16778 |
| I | DNA (125-mer) | dna | 125 | — | — |
| J | DNA (125-mer) | dna | 125 | — | — |
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 | 791 | 0.81 | 0.84 | 101 | empty |
| 2 | 93 | 0.76 | 0.96 | 23 | empty |
| 3 | 368 | 0.74 | 0.85 | 51 | empty |
| 4 | 89 | 0.73 | 0.95 | 24 | empty |
| 5 | 359 | 0.69 | 0.83 | 30 | empty |
Interfaces
36 interfaces between chains.
- I–J · 5744 Ų buried · 629 hydrogen bonds · nucleic-nucleic
- G–H · 2398 Ų buried · 34 hydrogen bonds · protein-protein
- C–D · 2386 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 2082 Ų buried · 19 hydrogen bonds · protein-protein
- E–F · 2068 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 6M4D · Structural mechanism of nucleosome dynamics governed by human histone variants H2A.B and… · the same entry in another collection · chain J against J, TM-score 1.00
- Q71UI9 · AlphaFold monomer V2.0 prediction for histone H2A.V (Q71UI9) · a predicted model of the same protein · chain C against A, TM-score 0.93
- Q16778 · AlphaFold monomer V2.0 prediction for histone H2B type 2-E (Q16778) · a predicted model of the same protein · chain D against A, TM-score 0.86
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 P68431
- Every structure of UniProt P62805
- Every structure of UniProt Q71UI9
- Every structure of UniProt Q16778
- Elsewhere: RCSB PDB 6M4D · PDBe 6M4D · UniProt P68431 · UniProt P62805 · UniProt Q71UI9 · UniProt Q16778
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