MolNFT v1 · #156440 · protein + DNA
Structural mechanism of nucleosome dynamics governed by human histone variants H2A.B and H2A.Z.2.2
6M4D · Histone H3.1: “Structural mechanism of nucleosome dynamics governed by human histone variants H2A.B and H2A.Z.2.2”. Electron microscopy, 20 pockets (best druggability 0.81). MolNFT v1 #156440 on GenesisL1: 3D structure, binding…
- 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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