MolNFT v1 · #156444 · protein + DNA
Structural mechanism of nucleosome dynamics governed by human histone variants H2A.B and H2A.Z.2.2
6M4H · DNA (103-mer): “Structural mechanism of nucleosome dynamics governed by human histone variants H2A.B and H2A.Z.2.2”. Electron microscopy, 20 pockets (best druggability 0.77). MolNFT v1 #156444 on GenesisL1: 3D structure, binding…
- PDB
- 6M4H
- Type
- protein + DNA
- Length
- 862 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (103-mer); Histone H3.1; Histone H4; Histone H2A-bbd type 2/3; Histone H2B type 2-E
- UniProt
- P68431, P62805, P0C5Z0, Q16778
- Pockets
- 20 · best druggability 0.77
Structure
electron microscopy · 6 distinct chains · 66% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| I | DNA (103-mer) | dna | 103 | — | — |
| J | DNA (103-mer) | dna | 103 | — | — |
| A, E | Histone H3.1 | protein | 74 | 72% helix, 5% strand | P68431 |
| B, F | Histone H4 | protein | 76 | 64% helix, 8% strand | P62805 |
| C, G | Histone H2A-bbd type 2/3 | protein | 90 | 52% helix, 4% strand | P0C5Z0 |
| D, H | Histone H2B type 2-E | protein | 88 | 76% helix, 1% strand | Q16778 |
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 777 | 0.77 | 0.82 | 60 | empty |
| 2 | 733 | 0.67 | 0.75 | 62 | empty |
| 3 | 500 | 0.61 | 0.75 | 42 | empty |
| 4 | 340 | 0.60 | 0.78 | 25 | empty |
| 5 | 342 | 0.59 | 0.77 | 22 | empty |
Interfaces
34 interfaces between chains.
- I–J · 4568 Ų buried · 457 hydrogen bonds · nucleic-nucleic
- G–H · 2498 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 2472 Ų buried · 17 hydrogen bonds · protein-protein
- E–F · 2039 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 2021 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6M4H · Structural mechanism of nucleosome dynamics governed by human histone variants H2A.B and… · the same entry in another collection · chain H against H, TM-score 1.00
- P0C5Z0 · AlphaFold monomer V2.0 prediction for histone H2A-bbd type 2/3 (P0C5Z0) · 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 0.89
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 P0C5Z0
- Every structure of UniProt Q16778
- Elsewhere: RCSB PDB 6M4H · PDBe 6M4H · UniProt P68431 · UniProt P62805 · UniProt P0C5Z0 · UniProt Q16778
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