4UDM: Im3

Crystal structure of Im3 in complex with Y52A mutant of E3RNase. Determined by X-ray diffraction at 2.96 Å resolution. Released 13 Jan 2016.

Method: X-ray diffraction
Resolution: 2.96 Å
Organism: ESCHERICHIA COLI BL21(DE3)
Chains: 2
Atoms: 1,490
Mol. weight: 20.79 kDa
Ligands: CA
Released: 13 Jan 2016

Explore 4UDM in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4UDM contains 11 α-helices and 15 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 4 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	3-11	9	1
β-strand	17-22	6	1
α-helix	23-25	3
α-helix	31-34	4
β-strand	44	1	1
β-strand	48-50	3	1
α-helix	55-59	5
α-helix	60-62	3
β-strand	72-80	9	1

Chain B: 7 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	6-8	3
α-helix	10-14	5
α-helix	15-17	3
β-strand	24-27	4	2
β-strand	32	1	1
α-helix	38	1
β-strand	39	1	1
α-helix	40-41	2
β-strand	42-45	4	2
α-helix	46-48	3
β-strand	50-55	6	2
β-strand	60-65	6	2
β-strand	70	1	3
β-strand	71-75	5	2
β-strand	82-84	3	2
β-strand	91	1	3
α-helix	93-95	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Colicin-E3 immunity protein	A	protein	85	ESCHERICHIA COLI BL21(DE3)	P02984 (AlphaFold model)
Colicin-E3	B	protein	96	ESCHERICHIA COLI BL21(DE3)	P00646 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4UDM_1 COLICIN-E3 IMMUNITY PROTEIN (chains A)
MGLKLDLTWFDKSTEDFKGEEYSKDFGDDGSVMESLGVPFKDNVNNGCFDVIAEWVPLLQ
PYFNHQIDISDNEYFVSFDYRDGDW

Sequence of entity 2 (B), FASTA

>4UDM_2 COLICIN-E3 (chains B)
GFKDYGHDYHPAPKTENIKGLGDLKPGIPKTPKQNGGGKRKRWTGDKGRKIAEWDSQHGE
LEGYRASDGQHLGSFDPKTGNQLKGPDPKRNIKKYL

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	3

Water and common crystallization additives (CL) are not listed.

Primary citation

Consequences of Inducing Intrinsic Disorder in a High-Affinity Protein-Protein Interaction. Papadakos, G., Sharma, A., Lancaster, L.E. et al. J Am Chem Soc (2015) 137:5252. DOI 10.1021/JA512607R · PubMed

Other PDB entries of the same protein (UniProt P02984 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3EIP 1.8 Å, Crystal structure of colicin E3 immunity protein: an inhibitor to a…
2B5U 2.3 Å, Crystal Structure Of Colicin E3 V206C Mutant In Complex With Its Immunity Protein
1E44 2.4 Å, ribonuclease domain of colicin E3 in complex with its immunity protein
1JCH 3.02 Å, Crystal Structure of Colicin E3 in Complex with its Immunity Protein

Browse structure collections

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