MolNFT v1 · #169235 · protein + DNA
The mouse cgas catalytic domain binding to human nucleosome that purified from HEK293T cells
6X5A · Histone H3.2: “The mouse cgas catalytic domain binding to human nucleosome that purified from HEK293T cells”. Electron microscopy, 1 ligand (ZN), 20 pockets (best druggability 0.82). MolNFT v1 #169235 on GenesisL1: 3D structure…
- PDB
- 6X5A
- Type
- protein + DNA
- Length
- 1,413 residues
- Chains
- 11
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3.2; Histone H4; Histone H2A type 1; Histone H2B type 1-C/E/F/G/I; DNA…
- EC
- 2.7.7.86
- UniProt
- Q71DI3, P62805, P0C0S8, P62807, Q8C6L5
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 10 distinct chains · 54% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Histone H3.2 | protein | 98 | 62% helix, 4% strand | Q71DI3 |
| B | Histone H4 | protein | 80 | 56% helix, 8% strand | P62805 |
| C | Histone H2A type 1 | protein | 108 | 52% helix, 6% strand | P0C0S8 |
| D | Histone H2B type 1-C/E/F/G/I | protein | 95 | 73% helix, 4% strand | P62807 |
| F | Histone H4 | protein | 81 | 60% helix, 9% strand | P62805 |
| G | Histone H2A type 1 | protein | 107 | 52% helix, 6% strand | P0C0S8 |
| H | Histone H2B type 1-C/E/F/G/I | protein | 94 | 70% helix, 4% strand | P62807 |
| I | DNA (natural) | dna | 145 | — | — |
| J | DNA (natural) | dna | 145 | — | — |
| K | Cyclic gmp-AMP synthase (EC 2.7.7.86) | protein | 362 | 42% helix, 18% strand | Q8C6L5 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 894 | 0.82 | 0.84 | 96 | empty |
| 2 | 1000 | 0.82 | 0.82 | 113 | empty |
| 3 | 1178 | 0.79 | 0.80 | 111 | empty |
| 4 | 257 | 0.71 | 0.87 | 34 | empty |
| 5 | 241 | 0.70 | 0.86 | 32 | empty |
Interfaces
37 interfaces between chains.
- I–J · 6560 Ų buried · 621 hydrogen bonds · nucleic-nucleic
- C–D · 2606 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 2558 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 2511 Ų buried · 13 hydrogen bonds · protein-protein
- G–H · 2494 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 6X5A · The mouse cGAS catalytic domain binding to human nucleosome that purified from HEK293T… · the same entry in another collection · chain K against K, TM-score 1.00
- Q71DI3 · AlphaFold monomer V2.0 prediction for histone H3.2 (Q71DI3) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q71DI3
- Every structure of UniProt P62805
- Every structure of UniProt P0C0S8
- Every structure of UniProt P62807
- Every structure of UniProt Q8C6L5
- Elsewhere: RCSB PDB 6X5A · PDBe 6X5A · UniProt Q71DI3 · UniProt P62805 · UniProt P0C0S8 · UniProt P62807 · UniProt Q8C6L5
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