MolNFT v1 · #41040 · protein
Crystal structure of the mutant N560A of the nuclease domain of COLE7 in complex with IM7
2JBG · Colicin-E7 immunity protein: “Crystal structure of the mutant N560A of the nuclease domain of COLE7 in complex with IM7”. X-ray diffraction, 2 ligands (ZN, SO4), 9 pockets (best druggability 0.69). MolNFT v1 #41040 on GenesisL1: 3D…
- PDB
- 2JBG
- Type
- protein
- Length
- 414 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, SO4
- Pockets
- 9 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Colicin-E7 immunity protein (EC 3.1.-.-) | protein | 86 | 58% helix, 0% strand | Q03708 |
| B, D | Colicin E7 (EC 3.1.-.-) | protein | 121 | 36% helix, 18% strand | Q47112 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 512 | 0.69 | 0.79 | 74 | empty |
| 2 | 155 | 0.47 | 0.77 | 25 | empty |
| 3 | 106 | 0.38 | 0.75 | 17 | empty |
| 4 | 95 | 0.37 | 0.76 | 13 | empty |
| 5 | 69 | 0.37 | 0.78 | 15 | empty |
Interfaces
6 interfaces between chains.
- A–B · 797 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 779 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 393 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 317 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 309 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 2JBG · crystal structure of the mutant N560A of the nuclease domain of ColE7 in complex with Im7 · the same entry in another collection · chain A against A, 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 2JBG · PDBe 2JBG · UniProt Q03708 · UniProt Q47112
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