MolNFT v1 · #40534 · protein + DNA
Crystal structure of the periplasmic endonuclease vvn complexed with a 16-bp DNA
2IVK · Endonuclease I: “Crystal structure of the periplasmic endonuclease vvn complexed with a 16-bp DNA”. X-ray diffraction, 15 pockets (best druggability 0.76). MolNFT v1 #40534 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 2IVK
- Type
- protein + DNA
- Length
- 938 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endonuclease I; 5'-D(*GP*AP*AP*TP*TP*CP*GP*AP*TP*CP *GP*AP*AP*TP*T)-3'…
- EC
- 3.1.-.-
- UniProt
- Q7MHK3
- Pockets
- 15 · best druggability 0.76
Structure
x-ray diffraction · 5 distinct chains · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Endonuclease I (EC 3.1.-.-) | protein | 210 | 44% helix, 14% strand | Q7MHK3 |
| B, C | Endonuclease I (EC 3.1.-.-) | protein | 213 | 46% helix, 15% strand | Q7MHK3 |
| E, G | 5'-D(*GP*AP*AP*TP*TP*CP*GP*AP*TP*CP *GP*AP*AP*TP*T)-3' | dna | 15 | — | — |
| F, H | 5'-D(*AP*AP*TP*TP*CP*GP*AP*TP*CP*GP *AP*AP*TP*TP*C)-3' | dna | 15 | — | — |
| I, J | 5'-D(*GP*AP*AP*TP*TP*CP*GP*AP*TP*CP *GP*AP*AP*TP*TP*C)-3' | dna | 16 | — | — |
Pockets
15 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 622 | 0.76 | 0.82 | 74 | empty |
| 2 | 529 | 0.76 | 0.83 | 35 | empty |
| 3 | 600 | 0.75 | 0.82 | 40 | empty |
| 4 | 800 | 0.73 | 0.78 | 42 | empty |
| 5 | 582 | 0.73 | 0.81 | 66 | empty |
Interfaces
23 interfaces between chains.
- E–F · 644 Ų buried · 54 hydrogen bonds · nucleic-nucleic
- G–H · 643 Ų buried · 53 hydrogen bonds · nucleic-nucleic
- I–J · 628 Ų buried · 39 hydrogen bonds · nucleic-nucleic
- A–F · 443 Ų buried · 8 hydrogen bonds · protein-nucleic
- D–H · 435 Ų buried · 8 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 2IVK · Crystal structure of the periplasmic endonuclease Vvn complexed with a 16-bp DNA · 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 Q7MHK3
- Elsewhere: RCSB PDB 2IVK · PDBe 2IVK · UniProt Q7MHK3
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