MolNFT v1 · #179354 · protein + DNA
Crystal structure of endonuclease Q complex with 27-mer duplex substrate with du at the active site
7K30: “Crystal structure of endonuclease Q complex with 27-mer duplex substrate with du at the active site”. X-ray diffraction, 2 ligands (ZN, MG), 4 pockets (best druggability 0.74). MolNFT v1 #179354 on GenesisL1: 3D structure, binding…
- PDB
- 7K30
- Type
- protein + DNA
- Length
- 449 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endonuclease Q; DNA (27-mer)
- UniProt
- I6V2I0
- Ligands
- ZN, MG
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endonuclease Q | protein | 395 | 35% helix, 19% strand | I6V2I0 |
| B | DNA (27-mer) | dna | 27 | — | — |
| C | DNA (27-mer) | dna | 27 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, C
- MG · Magnesium ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1163 | 0.74 | 0.77 | 97 | EDO |
| 2 | 152 | 0.44 | 0.76 | 17 | empty |
| 3 | 69 | 0.36 | 0.77 | 17 | empty |
| 4 | 53 | 0.26 | 0.74 | 12 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1201 Ų buried · 99 hydrogen bonds · nucleic-nucleic
- A–C · 860 Ų buried · 25 hydrogen bonds · protein-nucleic
- A–B · 559 Ų buried · 7 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 7K30 · Crystal structure of Endonuclease Q complex with 27-mer duplex substrate with dU at the… · 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 I6V2I0
- Elsewhere: RCSB PDB 7K30 · PDBe 7K30 · UniProt I6V2I0
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