MolNFT v1 · #174599 · protein + DNA
Human cgas-nucleosome complex
7C0M · Histone H3.1: “Human cgas-nucleosome complex”. Electron microscopy, 1 ligand (ZN), 20 pockets (best druggability 0.81). MolNFT v1 #174599 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7C0M
- Type
- protein + DNA
- Length
- 2,814 residues
- Chains
- 22
- 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
- 2.7.7.86
- UniProt
- P68431, P62805, P04908, P06899, Q8N884
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 11 distinct chains · 56% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, a | Histone H3.1 | protein | 97 | 66% helix, 4% strand | P68431 |
| B, b | Histone H4 | protein | 83 | 61% helix, 7% strand | P62805 |
| C, c | Histone H2A type 1-B/E | protein | 103 | 50% helix, 7% strand | P04908 |
| D, d | Histone H2B type 1-J | protein | 95 | 74% helix, 4% strand | P06899 |
| E, e | Histone H3.1 | protein | 97 | 64% helix, 4% strand | P68431 |
| F, f | Histone H4 | protein | 78 | 65% helix, 9% strand | P62805 |
| G, g | Histone H2A type 1-B/E | protein | 105 | 52% helix, 6% strand | P04908 |
| H, h | Histone H2B type 1-J | protein | 93 | 72% helix, 4% strand | P06899 |
| I, i | DNA (145-mer) | dna | 145 | — | — |
| J, j | DNA (145-mer) | dna | 145 | — | — |
| K, k | Cyclic gmp-AMP synthase (EC 2.7.7.86) | protein | 366 | 41% helix, 17% strand | Q8N884 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains K, 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 | 824 | 0.81 | 0.83 | 69 | empty |
| 2 | 650 | 0.79 | 0.85 | 69 | empty |
| 3 | 313 | 0.76 | 0.88 | 39 | empty |
| 4 | 1019 | 0.76 | 0.78 | 80 | empty |
| 5 | 378 | 0.76 | 0.87 | 43 | empty |
Interfaces
90 interfaces between chains.
- i–j · 6416 Ų buried · 528 hydrogen bonds · nucleic-nucleic
- I–J · 6407 Ų buried · 528 hydrogen bonds · nucleic-nucleic
- A–B · 2640 Ų buried · 18 hydrogen bonds · protein-protein
- a–b · 2638 Ų buried · 18 hydrogen bonds · protein-protein
- c–d · 2622 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 7C0M · Human cGAS-nucleosome complex · the same entry in another collection · chain K against K, 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 Q8N884
- Elsewhere: RCSB PDB 7C0M · PDBe 7C0M · UniProt P68431 · UniProt P62805 · UniProt P04908 · UniProt P06899 · UniProt Q8N884
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