Research workbench
355 bp di-nucleosome harboring cohesive DNA termini (high cryoprotectant)
Analyse 355 bp di-nucleosome harboring cohesive DNA termini (high cryoprotectant) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6M44
- Type
- protein + DNA
- Length
- 2,214 residues
- Chains
- 18
- 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 (355-mer)
- UniProt
- P68431, P62805, P04908, P06899
- Ligands
- CA
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 10 distinct chains · 66% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, K | Histone H3.1 | protein | 98 | 64% helix, 4% strand | P68431 |
| B, F, L, P | Histone H4 | protein | 79 | 65% helix, 9% strand | P62805 |
| C, G, M | Histone H2A type 1-B/E | protein | 103 | 59% helix, 7% strand | P04908 |
| D, N | Histone H2B type 1-J | protein | 95 | 73% helix, 4% strand | P06899 |
| H | Histone H2B type 1-J | protein | 94 | 73% helix, 4% strand | P06899 |
| I | DNA (355-mer) | dna | 355 | — | — |
| J | DNA (355-mer) | dna | 355 | — | — |
| O | Histone H3.1 | protein | 99 | 64% helix, 4% strand | P68431 |
| Q | Histone H2A type 1-B/E | protein | 106 | 58% helix, 7% strand | P04908 |
| R | Histone H2B type 1-J | protein | 96 | 72% helix, 4% strand | P06899 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains E, I, G, 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 | 833 | 0.80 | 0.83 | 72 | empty |
| 2 | 557 | 0.79 | 0.85 | 72 | empty |
| 3 | 469 | 0.78 | 0.86 | 60 | empty |
| 4 | 472 | 0.78 | 0.86 | 58 | empty |
| 5 | 571 | 0.77 | 0.84 | 52 | empty |
Interfaces
75 interfaces between chains.
- I–J · 15792 Ų buried · 1,442 hydrogen bonds · nucleic-nucleic
- Q–R · 2718 Ų buried · 32 hydrogen bonds · protein-protein
- C–D · 2714 Ų buried · 33 hydrogen bonds · protein-protein
- M–N · 2667 Ų buried · 26 hydrogen bonds · protein-protein
- G–H · 2664 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 6M44 · 355 bp di-nucleosome harboring cohesive DNA termini (high cryoprotectant) · the same entry in another collection · chain A against A, 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
- Elsewhere: RCSB PDB 6M44 · PDBe 6M44 · UniProt P68431 · UniProt P62805 · UniProt P04908 · UniProt P06899
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