MolNFT v1 · #24818 · protein
Structure of the E. COLI colicin D bound to its immunity protein immd
1V74: “Structure of the E. COLI colicin D bound to its immunity protein immd”. X-ray diffraction, 3 pockets (best druggability 0.48). MolNFT v1 #24818 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1V74
- Type
- protein
- Length
- 194 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Colicin D; Colicin D immunity protein
- UniProt
- P17998, P11899
- Pockets
- 3 · best druggability 0.48
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Colicin D | protein | 107 | 36% helix, 20% strand | P17998 |
| B | Colicin D immunity protein | protein | 87 | 62% helix, 2% strand | P11899 |
Ligands and binding sites
- 1PE · Pentaethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 144 | 0.48 | 0.78 | 26 | empty |
| 2 | 82 | 0.44 | 0.80 | 22 | empty |
| 3 | 83 | 0.39 | 0.78 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 1040 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 1V74 · Structure of the E. coli colicin D bound to its immunity protein ImmD · the same entry in another collection · chain A against A, TM-score 1.00
- P11899 · AlphaFold monomer V2.0 prediction for colicin-D immunity protein (P11899) · a predicted model of the same protein · chain B against A, TM-score 0.98
- P17998 · AlphaFold monomer V2.0 prediction for colicin-D (P17998) · 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 P17998
- Every structure of UniProt P11899
- Elsewhere: RCSB PDB 1V74 · PDBe 1V74 · UniProt P17998 · UniProt P11899
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