MolNFT v1 · #179452 · protein + DNA
Cryo-EM structure of 197BP nucleosome aided by scfv
7K61 · Histone H3.1: “Cryo-EM structure of 197BP nucleosome aided by scfv”. Electron microscopy, 20 pockets (best druggability 0.79). MolNFT v1 #179452 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7K61
- Type
- protein + DNA
- Length
- 1,616 residues
- Chains
- 12
- 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
- Pockets
- 20 · best druggability 0.79
Structure
electron microscopy · 7 distinct chains · 42% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Histone H3.1 | protein | 97 | 65% helix, 4% strand | P68431 |
| B, F | Histone H4 | protein | 83 | 60% helix, 8% 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 | — |
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 | 720 | 0.79 | 0.83 | 71 | empty |
| 2 | 456 | 0.76 | 0.85 | 49 | empty |
| 3 | 432 | 0.75 | 0.85 | 47 | empty |
| 4 | 372 | 0.71 | 0.83 | 35 | empty |
| 5 | 133 | 0.70 | 0.91 | 29 | empty |
Interfaces
39 interfaces between chains.
- I–J · 8867 Ų buried · 693 hydrogen bonds · nucleic-nucleic
- G–H · 2588 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 2578 Ų buried · 24 hydrogen bonds · protein-protein
- E–F · 2567 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 2560 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7K61 · Cryo-EM structure of 197bp nucleosome aided by scFv · the same entry in another collection · chain N against N, 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 7K61 · PDBe 7K61 · UniProt P68431 · UniProt P62805 · UniProt P04908 · UniProt P06899
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