MolNFT v1 · #38597 · protein + DNA
Structural basis for nucleic acid and toxin recognition of the bacterial antitoxin ccda
2H3A · 5'-D(P*AP*TP*AP*TP*GP*TP*AP*TP*AP*CP*CP*CP*G)-3': “Structural basis for nucleic acid and toxin recognition of the bacterial antitoxin ccda”. Solution nmr, 3 pockets (best druggability 0.55). MolNFT v1 #38597 on GenesisL1: 3D…
- PDB
- 2H3A
- Type
- protein + DNA
- Length
- 170 residues
- Chains
- 4
- Method
- solution nmr
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(P*AP*TP*AP*TP*GP*TP*AP*TP*AP*CP*CP*CP*G)-3'…
- UniProt
- Q9S0Z5
- Pockets
- 3 · best druggability 0.55
Structure
solution nmr · 3 distinct chains · 29% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | 5'-D(P*AP*TP*AP*TP*GP*TP*AP*TP*AP*CP*CP*CP*G)-3' | dna | 13 | — | — |
| D | 5'-D(P*TP*CP*GP*GP*GP*TP*AP*TP*AP*CP*AP*TP*A)-3' | dna | 13 | — | — |
| A, B | Ccda | protein | 72 | 29% helix, 8% strand | Q9S0Z5 |
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 300 | 0.55 | 0.75 | 30 | empty |
| 2 | 77 | 0.33 | 0.75 | 23 | empty |
| 3 | 65 | 0.32 | 0.76 | 14 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1815 Ų buried · 25 hydrogen bonds · protein-protein
- D–B · 675 Ų buried · 20 hydrogen bonds · protein-nucleic
- C–D · 639 Ų buried · 67 hydrogen bonds · nucleic-nucleic
- C–B · 502 Ų buried · 11 hydrogen bonds · protein-nucleic
- D–A · 302 Ų buried · 7 hydrogen bonds · protein-nucleic
Compared structures
- 2H3A · Structural basis for nucleic acid and toxin recognition of the bacterial antitoxin CcdA · the same entry in another collection · chain C against C, 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 Q9S0Z5
- Elsewhere: RCSB PDB 2H3A · PDBe 2H3A · UniProt Q9S0Z5
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