MolNFT v1 · #189995 · protein + DNA
Cryo-EM structure of nucleosome in complex with P300 acetyltransferase catalytic core (complex I)
7W9V · Histone H3.1: “Cryo-EM structure of nucleosome in complex with P300 acetyltransferase catalytic core (complex I)”. Electron microscopy, 20 pockets (best druggability 0.76). MolNFT v1 #189995 on GenesisL1: 3D structure, binding sites…
- PDB
- 7W9V
- Type
- protein + DNA
- Length
- 1,592 residues
- Chains
- 11
- 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 (145-mer)…
- EC
- 2.3.1.48, 2.3.1.-
- UniProt
- P68431, P62805, P04908, P06899, Q09472
- Pockets
- 20 · best druggability 0.76
Structure
electron microscopy · 11 distinct chains · 53% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone H3.1 | protein | 97 | 63% helix, 4% strand | P68431 |
| B | Histone H4 | protein | 83 | 61% helix, 8% strand | P62805 |
| C | Histone H2A type 1-B/E | protein | 103 | 52% helix, 6% strand | P04908 |
| D | Histone H2B type 1-J | protein | 95 | 74% helix, 4% strand | P06899 |
| E | Histone H3.1 | protein | 97 | 62% helix, 4% strand | P68431 |
| F | Histone H4 | protein | 78 | 65% helix, 8% strand | P62805 |
| G | Histone H2A type 1-B/E | protein | 105 | 53% helix, 7% strand | P04908 |
| H | Histone H2B type 1-J | protein | 93 | 75% helix, 4% strand | P06899 |
| I | DNA (145-mer) | dna | 145 | — | — |
| J | DNA (145-mer) | dna | 145 | — | — |
| K | Histone acetyltransferase P300 (EC 2.3.1.48, 2.3.1.-) | protein | 551 | 40% helix, 18% strand | Q09472 |
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 | 519 | 0.76 | 0.83 | 54 | empty |
| 2 | 409 | 0.74 | 0.85 | 44 | empty |
| 3 | 456 | 0.74 | 0.84 | 41 | empty |
| 4 | 443 | 0.73 | 0.84 | 46 | empty |
| 5 | 688 | 0.73 | 0.79 | 78 | empty |
Interfaces
41 interfaces between chains.
- I–J · 6480 Ų buried · 521 hydrogen bonds · nucleic-nucleic
- A–B · 2680 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 2636 Ų buried · 15 hydrogen bonds · protein-protein
- G–H · 2603 Ų buried · 17 hydrogen bonds · protein-protein
- E–F · 2543 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 7W9V · Cryo-EM structure of nucleosome in complex with p300 acetyltransferase catalytic core… · the same entry in another collection · chain K against K, TM-score 1.00
- Q09472 · AlphaFold monomer V2.0 prediction for histone acetyltransferase P300 (Q09472) · a predicted model of the same protein · chain K against A, TM-score 0.98
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 Q09472
- Elsewhere: RCSB PDB 7W9V · PDBe 7W9V · UniProt P68431 · UniProt P62805 · UniProt P04908 · UniProt P06899 · UniProt Q09472
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