9OFX: Proto-oncogene tyrosine-protein kinase Src

Crystal structure of c-Src SH3 domain in H32 space group mediated by nickel. Determined by X-ray diffraction at 1.45 Å resolution. Released 14 May 2025.

Method: X-ray diffraction
Resolution: 1.45 Å
Organism: Homo sapiens
Chains: 4
Atoms: 2,107
Mol. weight: 27.43 kDa
Ligands: NI
Released: 14 May 2025

Explore 9OFX in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9OFX contains 5 α-helices and 31 β-strands across 4 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.

Chains A and B: 1 helix, 8 β-strands

Element	Residues	Length	Sheet
β-strand	89-91	3	1
β-strand	95	1	2
β-strand	102	1	1
β-strand	105	1	2
β-strand	110-115	6	1
β-strand	121-126	6	1
β-strand	132-136	5	1
α-helix	137-139	3
β-strand	140-142	3	1

Chain C: 2 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	88-91	4	5
β-strand	95	1	6
β-strand	102	1	5
α-helix	103-104	2
β-strand	105	1	6
β-strand	110-114	5	5
β-strand	121-126	6	5
β-strand	132-136	5	5
α-helix	137-139	3
β-strand	140-142	3	5

Chain D: 1 helix, 7 β-strands

Element	Residues	Length	Sheet
β-strand	88-91	4	7
β-strand	95	1	8
β-strand	105	1	8
β-strand	110-113	4	7
β-strand	121-126	6	7
β-strand	132-136	5	7
α-helix	137-139	3
β-strand	140-142	3	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Proto-oncogene tyrosine-protein kinase Src	A, B, C, D	protein	59	Homo sapiens	P12931 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>9OFX_1 Proto-oncogene tyrosine-protein kinase Src (chains A, B, C, D)
GVTTFVALYDYESRTETDLSFKKGERLQIVNNTEGDWWLAHSLSTGQTGYIPSNYVAPS

Ligands and cofactors

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

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

Primary citation

Nickel Binding to the c-Src SH3 Domain Facilitates Crystallization. Calicdan, X., Fisher, O.S., Ha, B.H. et al. Protein Pept Lett (2025) 32:679-692. DOI 10.2174/0109298665417324250929120040 · PubMed

Other PDB entries of the same protein (UniProt P12931 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1FMK 1.5 Å, Crystal structure of human tyrosine-protein kinase C-src
1O43 1.5 Å, Crystal structure of SH2 in complex with RU82129.
1O4A 1.5 Å, Crystal structure of SH2 in complex with RU82197.
1O4R 1.5 Å, Crystal structure of SH2 in complex with RU78783.
2SRC 1.5 Å, Crystal structure of human tyrosine-protein kinase C-src, in complex with AMP-pnp
6C4S 1.5 Å, Human cSrc SH3 Domain in complex with Choline Kinase fragment 60-69
7NG7 1.5 Å, Src kinase bound to eCF506 trapped in inactive conformation
8VCF 1.5 Å, Crystal structure of Superbinder Src SH2 domain with Cysteine to Serine mutations
1O48 1.55 Å, Crystal structure of SH2 in complex with RU85053.
1O4G 1.55 Å, Crystal structure of SH2 in complex with DPI59.
1O4K 1.57 Å, Crystal structure of SH2 in complex with pasbn.
4F5B 1.57 Å, Triple mutant Src SH2 domain bound to phosphotyrosine

Browse structure collections

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