Research workbench
343 bp di-nucleosome harboring cohesive DNA termini assembled with linker histone H1.0
Analyse 343 bp di-nucleosome harboring cohesive DNA termini assembled with linker… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LA2
- Type
- protein + DNA
- Length
- 4,607 residues
- Chains
- 38
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3.1; Histone H4; Histone H2A type 1-B/E; Histone H2B type 1-J; DNA (343-mer)…
- UniProt
- P68431, P62805, P04908, P06899, P07305
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 19 distinct chains · 61% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| e, K, O, U | Histone H3.1 | protein | 99 | 67% helix, 4% strand | P68431 |
| f, L | Histone H4 | protein | 82 | 62% helix, 7% strand | P62805 |
| g, C, M, W | Histone H2A type 1-B/E | protein | 109 | 54% helix, 6% strand | P04908 |
| h, l, H, R, b | Histone H2B type 1-J | protein | 96 | 75% helix, 4% strand | P06899 |
| i, A, E, Y | Histone H3.1 | protein | 100 | 66% helix, 4% strand | P68431 |
| j | Histone H4 | protein | 81 | 64% helix, 9% strand | P62805 |
| k | Histone H2A type 1-B/E | protein | 108 | 55% helix, 6% strand | P04908 |
| I, c | DNA (343-mer) | dna | 343 | — | — |
| J, d | DNA (343-mer) | dna | 343 | — | — |
| B | Histone H4 | protein | 83 | 61% helix, 8% strand | P62805 |
| D, N | Histone H2B type 1-J | protein | 97 | 73% helix, 4% strand | P06899 |
| F, V | Histone H4 | protein | 84 | 61% helix, 8% strand | P62805 |
| G | Histone H2A type 1-B/E | protein | 104 | 57% helix, 7% strand | P04908 |
| S, T | Histone H1.0 | protein | 75 | 24% helix, 17% strand | P07305 |
| P | Histone H4 | protein | 86 | 59% helix, 8% strand | P62805 |
| Q | Histone H2A type 1-B/E | protein | 106 | 56% helix, 7% strand | P04908 |
| X | Histone H2B type 1-J | protein | 91 | 79% helix, 4% strand | P06899 |
| Z | Histone H4 | protein | 85 | 60% helix, 8% strand | P62805 |
| a | Histone H2A type 1-B/E | protein | 103 | 57% helix, 7% strand | P04908 |
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 | 1083 | 0.82 | 0.83 | 98 | empty |
| 2 | 838 | 0.80 | 0.83 | 85 | empty |
| 3 | 799 | 0.80 | 0.83 | 73 | empty |
| 4 | 766 | 0.79 | 0.83 | 73 | empty |
| 5 | 559 | 0.79 | 0.85 | 75 | empty |
Interfaces
177 interfaces between chains.
- c–d · 15508 Ų buried · 1,368 hydrogen bonds · nucleic-nucleic
- I–J · 15445 Ų buried · 1,310 hydrogen bonds · nucleic-nucleic
- O–P · 2806 Ų buried · 26 hydrogen bonds · protein-protein
- E–F · 2776 Ų buried · 29 hydrogen bonds · protein-protein
- Y–Z · 2744 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 6LA2 · 343 bp di-nucleosome harboring cohesive DNA termini assembled with linker histone H1.0 · 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 P68431
- Every structure of UniProt P62805
- Every structure of UniProt P04908
- Every structure of UniProt P06899
- Every structure of UniProt P07305
- Elsewhere: RCSB PDB 6LA2 · PDBe 6LA2 · UniProt P68431 · UniProt P62805 · UniProt P04908 · UniProt P06899 · UniProt P07305
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