MolNFT v1 · #17474 · protein + DNA
Crystal structure of the periplasmic endonuclease vvn complexed with octamer double stranded DNA
1OUP · 5'-D(*GP*CP*GP*AP*TP*CP*GP*C)-3': “Crystal structure of the periplasmic endonuclease vvn complexed with octamer double stranded DNA”. X-ray diffraction, 1 ligand (CA), 9 pockets (best druggability 0.80). MolNFT v1 #17474 on…
- PDB
- 1OUP
- Type
- protein + DNA
- Length
- 455 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*GP*CP*GP*AP*TP*CP*GP*C)-3'; 5'-D(*GP*CP*GP*AP*TP*C)-3'; 5'-D(P*GP*C)-3'; Nuclease
- EC
- 3.1.-.-
- UniProt
- Q8DCA6
- Ligands
- CA
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 5 distinct chains · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D, F | 5'-D(*GP*CP*GP*AP*TP*CP*GP*C)-3' | dna | 8 | — | — |
| E | 5'-D(*GP*CP*GP*AP*TP*C)-3' | dna | 6 | — | — |
| G | 5'-D(P*GP*C)-3' | dna | 2 | — | — |
| A | Nuclease (EC 3.1.-.-) | protein | 213 | 47% helix, 17% strand | Q8DCA6 |
| B | Nuclease (EC 3.1.-.-) | protein | 210 | 48% helix, 15% strand | Q8DCA6 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains E, G, A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1044 | 0.80 | 0.82 | 72 | empty |
| 2 | 254 | 0.63 | 0.81 | 41 | CA |
| 3 | 222 | 0.61 | 0.82 | 27 | empty |
| 4 | 106 | 0.51 | 0.82 | 22 | empty |
| 5 | 99 | 0.51 | 0.82 | 22 | empty |
Interfaces
12 interfaces between chains.
- A–B · 687 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 355 Ų buried · 32 hydrogen bonds · nucleic-nucleic
- F–A · 305 Ų buried · 4 hydrogen bonds · protein-nucleic
- G–A · 290 Ų buried · 6 hydrogen bonds · protein-nucleic
- E–F · 282 Ų buried · 29 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 1OUP · Crystal structure of the periplasmic endonuclease Vvn complexed with octamer double… · 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 Q8DCA6
- Elsewhere: RCSB PDB 1OUP · PDBe 1OUP · UniProt Q8DCA6
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