Research workbench
Crystal structure of the mutant N560D of the nuclease domain of COLE7 in complex with IM7
Analyse Crystal structure of the mutant N560D of the nuclease domain of COLE7 in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2JAZ
- Type
- protein
- Length
- 409 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Colicin E7 immunity protein; Colicin E7
- EC
- 3.1.-.-
- UniProt
- Q03708, Q47112
- Ligands
- ZN, PO4
- Pockets
- 10 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Colicin E7 immunity protein (EC 3.1.-.-) | protein | 85 | 59% helix, 0% strand | Q03708 |
| B | Colicin E7 (EC 3.1.-.-) | protein | 120 | 39% helix, 18% strand | Q47112 |
| D | Colicin E7 (EC 3.1.-.-) | protein | 119 | 42% helix, 17% strand | Q47112 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 521 | 0.69 | 0.79 | 76 | empty |
| 2 | 149 | 0.46 | 0.77 | 27 | empty |
| 3 | 111 | 0.38 | 0.75 | 19 | empty |
| 4 | 109 | 0.38 | 0.75 | 16 | empty |
| 5 | 95 | 0.38 | 0.76 | 14 | empty |
Interfaces
6 interfaces between chains.
- A–B · 794 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 784 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 398 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 322 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 317 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 2JAZ · Crystal structure of the mutant N560D of the nuclease domain of COLE7 in complex with IM7 · the same entry in another collection · chain C against C, TM-score 1.00
- Q03708 · AlphaFold monomer V2.0 prediction for colicin-E7 immunity protein (Q03708) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q47112 · AlphaFold monomer V2.0 prediction for colicin-E7 (Q47112) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q03708
- Every structure of UniProt Q47112
- Elsewhere: RCSB PDB 2JAZ · PDBe 2JAZ · UniProt Q03708 · UniProt Q47112
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