MolNFT v1 · #5599 · protein
Crystal structure of colicin E9 DNase domain with its cognate immunity protein IM9 (1.7 ångströms)
1EMV: “Crystal structure of colicin E9 DNase domain with its cognate immunity protein IM9 (1.7 ångströms)”. X-ray diffraction, 1 ligand (PO4), 1 pocket (best druggability 0.29). MolNFT v1 #5599 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1EMV
- Type
- protein
- Length
- 214 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Immunity protein IM9; Colicin E9
- EC
- 3.1.21.1
- UniProt
- P13479, P09883
- Ligands
- PO4
- Pockets
- 1 · best druggability 0.29
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Immunity protein IM9 | protein | 83 | 58% helix, 0% strand | P13479 |
| B | Colicin E9 (EC 3.1.21.1) | protein | 131 | 41% helix, 17% strand | P09883 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 75 | 0.29 | 0.73 | 17 | PO4 |
Interfaces
1 interface between chains.
- A–B · 814 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 1EMV · Crystal structure of colicin E9 DNase domain with its cognate immunity protein IM9 (1.7… · the same entry in another collection · chain A against A, TM-score 1.00
- P09883 · AlphaFold monomer V2.0 prediction for colicin-E9 (P09883) · a predicted model of the same protein · chain B against A, TM-score 0.98
- P13479 · AlphaFold monomer V2.0 prediction for colicin-E9 immunity protein (P13479) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P13479
- Every structure of UniProt P09883
- Elsewhere: RCSB PDB 1EMV · PDBe 1EMV · UniProt P13479 · UniProt P09883
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