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NMR structure analysis of the hematopoetic cell kinase SH3 domain complexed with an artificial high affinity ligand (PD1)

Analyse NMR structure analysis of the hematopoetic cell kinase SH3 domain complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
2OI3
Type
protein
Length
98 residues
Chains
2
Method
solution nmr
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Tyrosine-protein kinase hck; Artificial peptide PD1
EC
2.7.10.2
UniProt
P08631
Ligands
ACE, NH2

Structure

solution nmr · 2 distinct chains · 6% helix, 27% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
ATyrosine-protein kinase hck (EC 2.7.10.2)protein867% helix, 30% strandP08631
BArtificial peptide PD1protein120% helix, 0% strand—

Ligands and binding sites

  • ACE · Acetyl group · ligand · chains A, B
  • NH2 · Amino group · ion · chains B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Interfaces

1 interface between chains.

  • A–B · 654 Ų buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

  • 2OI3 · NMR Structure Analysis of the Hematopoetic Cell Kinase SH3 Domain complexed with an… · the same entry in another collection · chain A against A, TM-score 1.00
  • P08631 · AlphaFold monomer V2.0 prediction for tyrosine-protein kinase hck (P08631) · a predicted model of the same protein · chain A against A, TM-score 0.66

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