4HVU: T98D c-Src-SH3 domain mutant

Crystal structure of the T98D c-Src-SH3 domain mutant in complex with the high affinity peptide APP12. Determined by X-ray diffraction at 0.98 Å resolution. Released 1 May 2013.

Method: X-ray diffraction
Resolution: 0.98 Å
Organism: Gallus gallus
Chains: 2
Atoms: 650
Mol. weight: 8.28 kDa
Ligands: ACE
Released: 1 May 2013

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

Secondary structure: helices and β-sheets

4HVU contains 2 α-helices and 8 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: 1 helix, 8 β-strands

Element	Residues	Length	Sheet
β-strand	86-88	3	1
β-strand	92	1	2
β-strand	99	1	1
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, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2-9	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Proto-oncogene tyrosine-protein kinase Src	A	protein	61	Gallus gallus	P00523 (AlphaFold model)
SYNTHETIC PEPTIDE Acetyl-APPLPPRNRP	B	protein	11

Sequence of entity 1 (A), FASTA

>4HVU_1 Proto-oncogene tyrosine-protein kinase Src (chains A)
GSHMTFVALYDYESRTEDDLSFKKGERLQIVNNTEGDWWLAHSLTTGRTGYIPSNYVAPS
D

Sequence of entity 2 (B), FASTA

>4HVU_2 SYNTHETIC PEPTIDE Acetyl-APPLPPRNRP (chains B)
XAPPLPPRNRP

Ligands and cofactors

ID	Name	Formula	Copies
ACE	Acetyl group	C2 H4 O	2

Water and common crystallization additives (SO4) are not listed.

Primary citation

Atomic resolution structures of the c-Src SH3 domain in complex with two high-affinity peptides from classes I and II. Bacarizo, J., Camara-Artigas, A. Acta Crystallogr D Biol Crystallogr (2013) 69:756-766. DOI 10.1107/S0907444913001522 · 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
4HVW 0.98 Å, Crystal structure of the T98E c-Src-SH3 domain mutant in complex with the high affinity…
4OMO 1.04 Å, Crystal structure of the c-Src tyrosine kinase SH3 domain mutant Q128E
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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