MolNFT v1 · #59824 · protein
Model of histone octamer tubular crystals
3C9K · Histone H2A-IV: “Model of histone octamer tubular crystals”. Electron microscopy, 5 pockets (best druggability 0.75). MolNFT v1 #59824 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3C9K
- Type
- protein
- Length
- 724 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H2A-IV; Histone H2B 7; Histone H3.2; Histone H4
- UniProt
- P02263, P0C1H5, P84229, P62801
- Pockets
- 5 · best druggability 0.75
Structure
electron microscopy · 4 distinct chains · 67% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Histone H2A-IV | protein | 101 | 57% helix, 7% strand | P02263 |
| B, F | Histone H2B 7 | protein | 90 | 76% helix, 4% strand | P0C1H5 |
| C, G | Histone H3.2 | protein | 93 | 72% helix, 4% strand | P84229 |
| D, H | Histone H4 | protein | 78 | 64% helix, 9% strand | P62801 |
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 527 | 0.75 | 0.83 | 47 | empty |
| 2 | 468 | 0.74 | 0.83 | 44 | empty |
| 3 | 383 | 0.73 | 0.85 | 45 | empty |
| 4 | 94 | 0.49 | 0.82 | 17 | empty |
| 5 | 99 | 0.48 | 0.82 | 22 | empty |
Interfaces
19 interfaces between chains.
- E–F · 2600 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 2599 Ų buried · 31 hydrogen bonds · protein-protein
- G–H · 2486 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 2486 Ų buried · 17 hydrogen bonds · protein-protein
- C–E · 631 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3C9K · Model of Histone Octamer Tubular Crystals · the same entry in another collection · chain H against H, TM-score 1.00
- P84229 · AlphaFold monomer V2.0 prediction for histone H3.2 (P84229) · a predicted model of the same protein · chain C against A, TM-score 0.97
- P02263 · AlphaFold monomer V2.0 prediction for histone H2A-IV (P02263) · a predicted model of the same protein · chain A against A, TM-score 0.96
- P62801 · AlphaFold monomer V2.0 prediction for histone H4 (P62801) · a predicted model of the same protein · chain D against A, TM-score 0.95
- P0C1H5 · AlphaFold monomer V2.0 prediction for histone H2B 7 (P0C1H5) · a predicted model of the same protein · chain B against A, TM-score 0.90
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 P02263
- Every structure of UniProt P0C1H5
- Every structure of UniProt P84229
- Every structure of UniProt P62801
- Elsewhere: RCSB PDB 3C9K · PDBe 3C9K · UniProt P02263 · UniProt P0C1H5 · UniProt P84229 · UniProt P62801
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