Research workbench
349 bp di-nucleosome harboring cohesive DNA termini assembled with linker histone H1.0 (high cryoprotectant)
Analyse 349 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
- 6LA9
- Type
- protein + DNA
- Length
- 2,365 residues
- Chains
- 20
- 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 (349-mer)…
- UniProt
- P68431, P62805, P04908, P06899, P07305
- Ligands
- CA, K
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 11 distinct chains · 60% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, K | Histone H3.1 | protein | 99 | 65% helix, 4% strand | P68431 |
| B, L, P | Histone H4 | protein | 80 | 63% helix, 8% strand | P62805 |
| C, G, M | Histone H2A type 1-B/E | protein | 106 | 56% helix, 6% strand | P04908 |
| D, H, N, R | Histone H2B type 1-J | protein | 95 | 74% helix, 4% strand | P06899 |
| E, O | Histone H3.1 | protein | 98 | 65% helix, 4% strand | P68431 |
| F | Histone H4 | protein | 82 | 61% helix, 7% strand | P62805 |
| I | DNA (349-mer) | dna | 349 | — | — |
| J | DNA (349-mer) | dna | 349 | — | — |
| Q | Histone H2A type 1-B/E | protein | 106 | 56% helix, 6% strand | P04908 |
| S | Histone H1.0 | protein | 73 | 49% helix, 16% strand | P07305 |
| T | Histone H1.0 | protein | 74 | 49% helix, 16% strand | P07305 |
Ligands and binding sites
- CA · Calcium ion · metal · 40 copies · chains A, C, F, G, H, I, J, Q, S, O, P
- K · Potassium ion · metal · 2 copies · chains I, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 843 | 0.81 | 0.84 | 76 | empty |
| 2 | 876 | 0.80 | 0.83 | 74 | empty |
| 3 | 454 | 0.78 | 0.87 | 54 | empty |
| 4 | 509 | 0.78 | 0.86 | 57 | empty |
| 5 | 428 | 0.78 | 0.87 | 45 | empty |
Interfaces
78 interfaces between chains.
- I–J · 15659 Ų buried · 1,709 hydrogen bonds · nucleic-nucleic
- G–H · 2683 Ų buried · 29 hydrogen bonds · protein-protein
- E–F · 2672 Ų buried · 27 hydrogen bonds · protein-protein
- M–N · 2611 Ų buried · 24 hydrogen bonds · protein-protein
- Q–R · 2607 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 6LA9 · 349 bp di-nucleosome harboring cohesive DNA termini assembled with linker histone H1.0… · the same entry in another collection · chain T against T, 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 6LA9 · PDBe 6LA9 · UniProt P68431 · UniProt P62805 · UniProt P04908 · UniProt P06899 · UniProt P07305
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