MolNFT v1 · #141706 · protein + DNA
The crystal structure of kacta-DNA complex
5ZGN · Kaca: “The crystal structure of kacta-DNA complex”. X-ray diffraction, 1 ligand (SO4), 8 pockets (best druggability 0.70). MolNFT v1 #141706 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5ZGN
- Type
- protein + DNA
- Length
- 674 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kaca; Kact; DNA (27-mer)
- UniProt
- A0A0H3GLZ1, A0A0H3GMP0
- Ligands
- SO4
- Pockets
- 8 · best druggability 0.70
Structure
x-ray diffraction · 5 distinct chains · 51% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Kaca | protein | 69 | 71% helix, 10% strand | A0A0H3GLZ1 |
| B, E | Kaca | protein | 82 | 68% helix, 13% strand | A0A0H3GLZ1 |
| C, F | Kact | protein | 159 | 34% helix, 31% strand | A0A0H3GMP0 |
| G | DNA (27-mer) | dna | 27 | — | — |
| H | DNA (27-mer) | dna | 27 | — | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains A, C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 706 | 0.70 | 0.78 | 77 | empty |
| 2 | 382 | 0.62 | 0.78 | 46 | SO4 |
| 3 | 360 | 0.60 | 0.77 | 44 | SO4 |
| 4 | 230 | 0.49 | 0.75 | 24 | empty |
| 5 | 214 | 0.48 | 0.75 | 16 | empty |
Interfaces
25 interfaces between chains.
- E–F · 1889 Ų buried · 32 hydrogen bonds · protein-protein
- B–C · 1848 Ų buried · 26 hydrogen bonds · protein-protein
- D–E · 1786 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1782 Ų buried · 18 hydrogen bonds · protein-protein
- G–H · 1203 Ų buried · 104 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 14 modified (engineered).
Compared structures
- 5ZGN · The crystal structure of KacTA-DNA complex · the same entry in another collection · chain A against A, 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 A0A0H3GLZ1
- Every structure of UniProt A0A0H3GMP0
- Elsewhere: RCSB PDB 5ZGN · PDBe 5ZGN · UniProt A0A0H3GLZ1 · UniProt A0A0H3GMP0
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