Research workbench
Crystal structure of the periplasmic endonuclease vvn complexed with octamer double stranded DNA
Analyse Crystal structure of the periplasmic endonuclease vvn complexed with octamer… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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