Research workbench
355 bp di-nucleosome harboring cohesive DNA termini
Analyse 355 bp di-nucleosome harboring cohesive DNA termini in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6M3V
- Type
- protein + DNA
- Length
- 2,211 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, K
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 9 distinct chains · 67% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, K, O | Histone H3.1 | protein | 98 | 67% helix, 4% strand | P68431 |
| B, F, L, P | Histone H4 | protein | 79 | 66% 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 | 74% helix, 4% strand | P06899 |
| H | Histone H2B type 1-J | protein | 94 | 74% helix, 4% strand | P06899 |
| I | DNA (355-mer) | dna | 355 | — | — |
| J | DNA (355-mer) | dna | 355 | — | — |
| Q | Histone H2A type 1-B/E | protein | 104 | 59% helix, 7% strand | P04908 |
| R | Histone H2B type 1-J | protein | 96 | 73% helix, 4% strand | P06899 |
Ligands and binding sites
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 | 946 | 0.84 | 0.85 | 120 | empty |
| 2 | 845 | 0.81 | 0.84 | 77 | empty |
| 3 | 848 | 0.80 | 0.83 | 79 | empty |
| 4 | 390 | 0.76 | 0.86 | 47 | empty |
| 5 | 397 | 0.75 | 0.86 | 50 | empty |
Interfaces
75 interfaces between chains.
- I–J · 15605 Ų buried · 1,397 hydrogen bonds · nucleic-nucleic
- Q–R · 2720 Ų buried · 28 hydrogen bonds · protein-protein
- M–N · 2689 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 2685 Ų buried · 28 hydrogen bonds · protein-protein
- G–H · 2659 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 6M3V · 355 bp di-nucleosome harboring cohesive DNA termini · the same entry in another collection · chain E against E, 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 6M3V · PDBe 6M3V · UniProt P68431 · UniProt P62805 · UniProt P04908 · UniProt P06899
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