MolNFT v1 · #118241 · protein
Crystal structure of colicin E9 in complex with its immunity protein IM9
5EW5 · Colicin-E9: “Crystal structure of colicin E9 in complex with its immunity protein IM9”. X-ray diffraction, 20 pockets (best druggability 0.78). MolNFT v1 #118241 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5EW5
- Type
- protein
- Length
- 2,269 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Colicin-E9; Colicin-E9 immunity protein
- EC
- 3.1.-.-
- UniProt
- P09883, P13479
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Colicin-E9 (EC 3.1.-.-) | protein | 490 | 45% helix, 21% strand | P09883 |
| E, F | Colicin-E9 immunity protein | protein | 83 | 59% helix, 0% strand | P13479 |
| G | Colicin-E9 immunity protein | protein | 73 | 67% helix, 0% strand | P13479 |
| H | Colicin-E9 immunity protein | protein | 70 | 56% helix, 0% strand | P13479 |
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1059 | 0.78 | 0.80 | 99 | empty |
| 2 | 1184 | 0.77 | 0.79 | 115 | empty |
| 3 | 1180 | 0.76 | 0.78 | 98 | empty |
| 4 | 920 | 0.75 | 0.78 | 73 | empty |
| 5 | 606 | 0.74 | 0.81 | 67 | empty |
Interfaces
14 interfaces between chains.
- B–C · 1992 Ų buried · 28 hydrogen bonds · protein-protein
- A–D · 1978 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 1307 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 1296 Ų buried · 14 hydrogen bonds · protein-protein
- B–F · 1011 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5EW5 · Crystal Structure of Colicin E9 In Complex with Its Immunity Protein Im9 · the same entry in another collection · chain H against H, TM-score 1.00
- P09883 · AlphaFold monomer V2.0 prediction for colicin-E9 (P09883) · a predicted model of the same protein · chain A 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 G 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 P09883
- Every structure of UniProt P13479
- Elsewhere: RCSB PDB 5EW5 · PDBe 5EW5 · UniProt P09883 · UniProt P13479
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