MolNFT v1 · #156443 · protein + DNA
Structural mechanism of nucleosome dynamics governed by human histone variants H2A.B and H2A.Z.2.2
6M4G · DNA (93-mer): “Structural mechanism of nucleosome dynamics governed by human histone variants H2A.B and H2A.Z.2.2”. Electron microscopy, 20 pockets (best druggability 0.78). MolNFT v1 #156443 on GenesisL1: 3D structure, binding…
- PDB
- 6M4G
- Type
- protein + DNA
- Length
- 842 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (93-mer); Histone H3.1; Histone H4; Histone H2B type 2-E; Histone H2A-bbd type 2/3
- UniProt
- P68431, P62805, Q16778, P0C5Z0
- Pockets
- 20 · best druggability 0.78
Structure
electron microscopy · 6 distinct chains · 67% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| I | DNA (93-mer) | dna | 93 | — | — |
| J | DNA (93-mer) | dna | 93 | — | — |
| A, E | Histone H3.1 | protein | 74 | 72% helix, 5% strand | P68431 |
| B, F | Histone H4 | protein | 76 | 64% helix, 8% strand | P62805 |
| D, H | Histone H2B type 2-E | protein | 88 | 76% helix, 1% strand | Q16778 |
| C, G | Histone H2A-bbd type 2/3 | protein | 90 | 57% helix, 4% strand | P0C5Z0 |
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 819 | 0.78 | 0.82 | 72 | empty |
| 2 | 620 | 0.66 | 0.76 | 47 | empty |
| 3 | 379 | 0.62 | 0.78 | 39 | empty |
| 4 | 495 | 0.61 | 0.75 | 34 | empty |
| 5 | 349 | 0.58 | 0.76 | 26 | empty |
Interfaces
34 interfaces between chains.
- I–J · 4284 Ų buried · 304 hydrogen bonds · nucleic-nucleic
- D–C · 2413 Ų buried · 17 hydrogen bonds · protein-protein
- H–G · 2396 Ų buried · 17 hydrogen bonds · protein-protein
- E–F · 2024 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 2022 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6M4G · Structural mechanism of nucleosome dynamics governed by human histone variants H2A.B and… · the same entry in another collection · chain G against G, 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 0.92
- 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 Q16778
- Every structure of UniProt P0C5Z0
- Elsewhere: RCSB PDB 6M4G · PDBe 6M4G · UniProt P68431 · UniProt P62805 · UniProt Q16778 · UniProt P0C5Z0
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