4OMO: C-Src tyrosine kinase SH3 domain mutant Q128E

Crystal structure of the c-Src tyrosine kinase SH3 domain mutant Q128E. Determined by X-ray diffraction at 1.04 Å resolution. Released 10 Dec 2014.

Method: X-ray diffraction
Resolution: 1.04 Å
Organism: Gallus gallus
Chains: 2
Atoms: 1,175
Mol. weight: 14.17 kDa
Ligands: NI
Released: 10 Dec 2014

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

Secondary structure: helices and β-sheets

4OMO contains 3 α-helices and 16 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: 2 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	86-88	3	1
β-strand	92	1	2
β-strand	99	1	1
α-helix	100-101	2
β-strand	102	1	2
β-strand	107-112	6	1
β-strand	118-123	6	1
β-strand	129-133	5	1
α-helix	134-136	3
β-strand	137-139	3	1

Chain B: 1 helix, 8 β-strands

Element	Residues	Length	Sheet
β-strand	85-88	4	3
β-strand	92	1	4
β-strand	99	1	3
β-strand	102	1	4
β-strand	107-110	4	3
β-strand	118-123	6	3
β-strand	129-133	5	3
α-helix	134-136	3
β-strand	137-139	3	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Proto-oncogene tyrosine-protein kinase Src	A, B	protein	61	Gallus gallus	P00523 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4OMO_1 Proto-oncogene tyrosine-protein kinase Src (chains A, B)
GSHMTFVALYDYESRTETDLSFKKGERLQIVNNTEGDWWLAHSLTTGETGYIPSNYVAPS
D

Ligands and cofactors

ID	Name	Formula	Copies
NI	Nickel (II) ion	Ni	2

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

Primary citation

Electrostatic Effects in the Folding of the SH3 Domain of the c-Src Tyrosine Kinase: pH-Dependence in 3D-Domain Swapping and Amyloid Formation. Bacarizo, J., Martinez-Rodriguez, S., Martin-Garcia, J.M. et al. PLoS One (2014) 9:e113224-e113224. DOI 10.1371/journal.pone.0113224 · PubMed

Other PDB entries of the same protein (UniProt P00523 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6XVM 0.9 Å, Crystal structure of c-Src SH3 domain without ATCUN motif: monomer 2
7A31 0.94 Å, Crystal structure of the c-Src SH3 domain mutant S94A-T98D-V111L-N113S-T114S at pH 4.5
5OAV 0.95 Å, High resolution crystal structure of the c-Src-SH3 domain mutant E93V in complex with…
7A33 0.96 Å, Crystal structure of the c-Src SH3 domain mutant S94A-T98D-V111L-N113S-T114S at pH 3.0
4RTZ 0.98 Å, Crystal structure of the c-Src-SH3 domain in complex with the high affinity peptide VSL12
4HVU 0.98 Å, Crystal structure of the T98D c-Src-SH3 domain mutant in complex with the high affinity…
4HVW 0.98 Å, Crystal structure of the T98E c-Src-SH3 domain mutant in complex with the high affinity…
6XX4 1.05 Å, Crystal structure of the c-Src SH3 domain H122R-Q128E mutant in complex with Ni(II) at…
4HVV 1.1 Å, Crystal structure of the T98E c-Src-SH3 domain mutant in complex with the high affinity…
7A32 1.15 Å, Crystal structure of the c-Src SH3 domain mutant S94A-T98D-V111L-N113S-T114S at pH 7.0
5ECA 1.16 Å, Crystal structure of a chimeric c-Src-SH3 domain with the sequence of the RT-loop from…
5OB0 1.17 Å, Crystal structure of the c-Src-SH3 domain Q128E mutant in complex with the high affinity…

Browse structure collections

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