MolNFT v1 · #155336 · protein + DNA
H3-H3-H3 tri-nucleosome with the 22 base-pair linker DNA
6L4A · Histone H3.1: “H3-H3-H3 tri-nucleosome with the 22 base-pair linker DNA”. Electron microscopy, 20 pockets (best druggability 0.78). MolNFT v1 #155336 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6L4A
- Type
- protein + DNA
- Length
- 3,223 residues
- Chains
- 26
- Method
- electron microscopy
- 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 (485-mer)
- UniProt
- P68431, P62805, P04908, P06899
- Pockets
- 20 · best druggability 0.78
Structure
electron microscopy · 10 distinct chains · 63% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, K, S | Histone H3.1 | protein | 97 | 66% helix, 4% strand | P68431 |
| B, L, T | Histone H4 | protein | 83 | 59% helix, 8% strand | P62805 |
| C, M, U | Histone H2A type 1-B/E | protein | 103 | 54% helix, 7% strand | P04908 |
| D, N, V | Histone H2B type 1-J | protein | 95 | 74% helix, 4% strand | P06899 |
| E, O, W | Histone H3.1 | protein | 97 | 64% helix, 4% strand | P68431 |
| F, P, X | Histone H4 | protein | 78 | 59% helix, 9% strand | P62805 |
| G, Q, Y | Histone H2A type 1-B/E | protein | 105 | 52% helix, 7% strand | P04908 |
| H, R, Z | Histone H2B type 1-J | protein | 93 | 75% helix, 4% strand | P06899 |
| I | DNA (485-mer) | dna | 485 | — | — |
| J | DNA (485-mer) | dna | 485 | — | — |
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 | 548 | 0.78 | 0.85 | 66 | empty |
| 2 | 483 | 0.77 | 0.85 | 59 | empty |
| 3 | 514 | 0.77 | 0.85 | 65 | empty |
| 4 | 1143 | 0.75 | 0.78 | 74 | empty |
| 5 | 375 | 0.75 | 0.86 | 41 | empty |
Interfaces
107 interfaces between chains.
- I–J · 21757 Ų buried · 1,724 hydrogen bonds · nucleic-nucleic
- S–T · 2673 Ų buried · 29 hydrogen bonds · protein-protein
- K–L · 2670 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 2659 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 2637 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 6L4A · H3-H3-H3 tri-nucleosome with the 22 base-pair linker DNA · 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 6L4A · PDBe 6L4A · UniProt P68431 · UniProt P62805 · UniProt P04908 · UniProt P06899
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