Research workbench

Crystal structure of colicin E9 in complex with its immunity protein IM9

Analyse Crystal structure of colicin E9 in complex with its immunity protein IM9 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

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.

Pocket	Volume (Å³)	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 Å² buried · 28 hydrogen bonds · protein-protein
A–D · 1978 Å² buried · 24 hydrogen bonds · protein-protein
A–C · 1307 Å² buried · 13 hydrogen bonds · protein-protein
B–D · 1296 Å² buried · 14 hydrogen bonds · protein-protein
B–F · 1011 Å² 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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