Research workbench
Crystal structure of the nuclease domain of COLE7 (H545Q mutant) in complex with an 18-bp duplex DNA
Analyse Crystal structure of the nuclease domain of COLE7 (H545Q mutant) in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2IVH
- Type
- protein + DNA
- Length
- 160 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Colcin-E7; 5'-D(*GP*GP*AP*AP*TP*TP*CP*GP*AP*TP *CP*GP*AP*AP*TP*TP*CP*C)-3'
- EC
- 3.1.-.-
- UniProt
- Q47112
- Ligands
- ZN
- Pockets
- 5 · best druggability 0.51
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Colcin-E7 (EC 3.1.-.-) | protein | 124 | 34% helix, 19% strand | Q47112 |
| B, C | 5'-D(*GP*GP*AP*AP*TP*TP*CP*GP*AP*TP *CP*GP*AP*AP*TP*TP*CP*C)-3' | dna | 18 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 157 | 0.51 | 0.79 | 22 | empty |
| 2 | 166 | 0.45 | 0.75 | 17 | empty |
| 3 | 81 | 0.43 | 0.80 | 14 | empty |
| 4 | 99 | 0.41 | 0.78 | 14 | empty |
| 5 | 62 | 0.29 | 0.74 | 18 | empty |
Interfaces
3 interfaces between chains.
- B–C · 799 Ų buried · 72 hydrogen bonds · nucleic-nucleic
- A–B · 474 Ų buried · 14 hydrogen bonds · protein-nucleic
- A–C · 412 Ų buried · 5 hydrogen bonds · protein-nucleic
Compared structures
- 2IVH · Crystal structure of the nuclease domain of ColE7 (H545Q mutant) in complex with an 18-bp… · the same entry in another collection · chain A against A, TM-score 1.00
- Q47112 · AlphaFold monomer V2.0 prediction for colicin-E7 (Q47112) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 Q47112
- Elsewhere: RCSB PDB 2IVH · PDBe 2IVH · UniProt Q47112
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