MolNFT v1 · #179449 · protein + DNA
Cryo-EM structure of a chromatosome containing human linker histone H1.4
7K5Y · Histone H3.1: “Cryo-EM structure of a chromatosome containing human linker histone H1.4”. Electron microscopy, 20 pockets (best druggability 0.79). MolNFT v1 #179449 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7K5Y
- Type
- protein + DNA
- Length
- 1,691 residues
- Chains
- 13
- 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 (197-mer)…
- UniProt
- P68431, P62805, P04908, P06899, P10412
- Pockets
- 20 · best druggability 0.79
Structure
electron microscopy · 8 distinct chains · 43% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Histone H3.1 | protein | 97 | 66% helix, 4% strand | P68431 |
| B, F | Histone H4 | protein | 83 | 60% helix, 7% strand | P62805 |
| C, G | Histone H2A type 1-B/E | protein | 109 | 55% helix, 6% strand | P04908 |
| D, H | Histone H2B type 1-J | protein | 95 | 73% helix, 4% strand | P06899 |
| I | DNA (197-mer) | dna | 197 | — | — |
| J | DNA (197-mer) | dna | 197 | — | — |
| M, N | SCFV20 | protein | 227 | 5% helix, 52% strand | — |
| U | Histone H1.4 | protein | 75 | 53% helix, 12% strand | P10412 |
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 | 1109 | 0.79 | 0.81 | 86 | empty |
| 2 | 477 | 0.76 | 0.84 | 44 | empty |
| 3 | 438 | 0.73 | 0.84 | 47 | empty |
| 4 | 488 | 0.71 | 0.81 | 41 | empty |
| 5 | 778 | 0.70 | 0.77 | 74 | empty |
Interfaces
41 interfaces between chains.
- I–J · 8921 Ų buried · 683 hydrogen bonds · nucleic-nucleic
- C–D · 2581 Ų buried · 21 hydrogen bonds · protein-protein
- G–H · 2565 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 2564 Ų buried · 21 hydrogen bonds · protein-protein
- E–F · 2561 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 7K5Y · Cryo-EM structure of a chromatosome containing human linker histone H1.4 · the same entry in another collection · chain U against U, 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 P10412
- Elsewhere: RCSB PDB 7K5Y · PDBe 7K5Y · UniProt P68431 · UniProt P62805 · UniProt P04908 · UniProt P06899 · UniProt P10412
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