Research workbench
H3-CA-H3 tri-nucleosome with the 22 base-pair linker DNA
Analyse H3-CA-H3 tri-nucleosome with the 22 base-pair linker DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6L49
- Type
- protein + DNA
- Length
- 3,178 residues
- Chains
- 26
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 18.9
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- Histone H3-like centromeric protein A; Histone H4; Histone H2A type 1-B/E; Histone H2B…
- UniProt
- P49450, P62805, P04908, P06899, P68431
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · resolution 18.9 · 16 distinct chains · 61% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone H3-like centromeric protein A | protein | 89 | 53% helix, 3% strand | P49450 |
| B, P, X | Histone H4 | protein | 78 | 62% helix, 5% strand | P62805 |
| C | Histone H2A type 1-B/E | protein | 97 | 57% helix, 5% strand | P04908 |
| D, H | Histone H2B type 1-J | protein | 90 | 66% helix, 3% strand | P06899 |
| E | Histone H3-like centromeric protein A | protein | 83 | 61% helix, 4% strand | P49450 |
| F | Histone H4 | protein | 79 | 62% helix, 6% strand | P62805 |
| G | Histone H2A type 1-B/E | protein | 100 | 54% helix, 5% strand | P04908 |
| I | DNA (485-mer) | dna | 485 | — | — |
| J | DNA (485-mer) | dna | 485 | — | — |
| K, S | Histone H3.1 | protein | 97 | 66% helix, 3% strand | P68431 |
| L, T | Histone H4 | protein | 83 | 55% helix, 7% strand | P62805 |
| M, U | Histone H2A type 1-B/E | protein | 103 | 50% helix, 7% strand | P04908 |
| N, V | Histone H2B type 1-J | protein | 95 | 74% helix, 4% strand | P06899 |
| O, W | Histone H3.1 | protein | 97 | 62% helix, 3% strand | P68431 |
| Q, Y | Histone H2A type 1-B/E | protein | 105 | 53% helix, 7% strand | P04908 |
| R, Z | Histone H2B type 1-J | protein | 93 | 74% helix, 4% strand | P06899 |
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 | 945 | 0.82 | 0.84 | 92 | empty |
| 2 | 533 | 0.77 | 0.84 | 61 | empty |
| 3 | 575 | 0.76 | 0.83 | 54 | empty |
| 4 | 453 | 0.75 | 0.84 | 51 | empty |
| 5 | 519 | 0.75 | 0.83 | 47 | empty |
Interfaces
108 interfaces between chains.
- I–J · 22095 Ų buried · 1,500 hydrogen bonds · nucleic-nucleic
- S–T · 2663 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 2645 Ų buried · 18 hydrogen bonds · protein-protein
- G–H · 2634 Ų buried · 18 hydrogen bonds · protein-protein
- M–N · 2627 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 6L49 · H3-ca-H3 tri-nucleosome with the 22 base-pair linker DNA · the same entry in another collection · chain J against J, TM-score 1.00
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 P62805
- Every structure of UniProt P04908
- Every structure of UniProt P06899
- Every structure of UniProt P68431
- Elsewhere: RCSB PDB 6L49 · PDBe 6L49 · UniProt P49450 · UniProt P62805 · UniProt P04908 · UniProt P06899 · UniProt P68431
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