MolNFT v1 · #155524 · protein + DNA
169 bp nucleosome, harboring cohesive DNA termini, assembled with linker histone H1.0
6LAB · Histone H3.1: “169 bp nucleosome, harboring cohesive DNA termini, assembled with linker histone H1.0”. X-ray diffraction, 3 ligands (CA, K, CL), 20 pockets (best druggability 0.80). MolNFT v1 #155524 on GenesisL1: 3D structure…
- PDB
- 6LAB
- Type
- protein + DNA
- Length
- 2,416 residues
- Chains
- 22
- 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 (169-mer)…
- UniProt
- P68431, P62805, P04908, P06899, P07305
- Ligands
- CA, K, CL
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 13 distinct chains · 54% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, K, O | Histone H3.1 | protein | 98 | 67% helix, 4% strand | P68431 |
| B | Histone H4 | protein | 80 | 63% helix, 9% strand | P62805 |
| C | Histone H2A type 1-B/E | protein | 105 | 57% helix, 7% strand | P04908 |
| D, H, N, R | Histone H2B type 1-J | protein | 96 | 74% helix, 4% strand | P06899 |
| F | Histone H4 | protein | 85 | 61% helix, 8% strand | P62805 |
| G, Q | Histone H2A type 1-B/E | protein | 103 | 55% helix, 7% strand | P04908 |
| I, S | DNA (169-mer) | dna | 169 | — | — |
| J, T | DNA (169-mer) | dna | 169 | — | — |
| L | Histone H4 | protein | 83 | 60% helix, 7% strand | P62805 |
| M | Histone H2A type 1-B/E | protein | 106 | 55% helix, 7% strand | P04908 |
| P | Histone H4 | protein | 86 | 58% helix, 8% strand | P62805 |
| U | Histone H1.0 | protein | 104 | 28% helix, 9% strand | P07305 |
| V | Histone H1.0 | protein | 109 | 28% helix, 6% strand | P07305 |
Ligands and binding sites
- CA · Calcium ion · metal · 20 copies · chains C, D, I, J, M, N, S, T
- K · Potassium ion · metal · 2 copies · chains C, D, G, M, Q, R
- CL · Chloride ion · ion · 2 copies · chains M, N, Q, R
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 | 718 | 0.80 | 0.84 | 65 | K |
| 2 | 709 | 0.79 | 0.84 | 71 | empty |
| 3 | 736 | 0.79 | 0.83 | 74 | K |
| 4 | 411 | 0.77 | 0.86 | 52 | empty |
| 5 | 514 | 0.76 | 0.84 | 49 | empty |
Interfaces
86 interfaces between chains.
- I–J · 7556 Ų buried · 687 hydrogen bonds · nucleic-nucleic
- S–T · 7503 Ų buried · 685 hydrogen bonds · nucleic-nucleic
- O–P · 2746 Ų buried · 31 hydrogen bonds · protein-protein
- G–H · 2671 Ų buried · 25 hydrogen bonds · protein-protein
- Q–R · 2666 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 6LAB · 169 bp nucleosome, harboring cohesive DNA termini, assembled with linker histone H1.0 · the same entry in another collection · chain S against S, 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 6LAB · PDBe 6LAB · UniProt P68431 · UniProt P62805 · UniProt P04908 · UniProt P06899 · UniProt P07305
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