SMTL ID : 9ofx.1

Crystal structure of c-Src SH3 domain in H32 space group mediated by nickel

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-tetramer

Ligands

2 x NI: NICKEL (II) ION(Non-covalent)

NI.1: 2 residues within 4Å: Chain A: G.1 Chain B: H.41 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: A:G.1, B:H.41, H2O.1, H2O.1, H2O.1 NI.4: 3 residues within 4Å: Chain A: H.41 Chain B: G.1, V.2 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: B:G.1, A:H.41, H2O.2, H2O.2, H2O.2

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: S.13, L.19, S.20, Q.47 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.13, A:S.13, A:S.20, A:S.20, A:Q.47 Water bridges: A:S.13 GOL.3: 3 residues within 4Å: Chain A: Y.9, N.54, Y.55 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.54, A:Y.55 GOL.5: 5 residues within 4Å: Chain A: L.43, S.44, T.45, G.46 Chain B: G.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.45 Water bridges: A:G.46, A:G.46 GOL.6: 3 residues within 4Å: Chain C: G.35, D.36, W.37 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.36, C:W.37, C:W.37 GOL.7: 3 residues within 4Å: Chain C: Y.9, N.54, Y.55 3 PLIP interactions: 3 interactions with chain C Water bridges: C:D.10, C:N.54, C:Y.55 GOL.8: 3 residues within 4Å: Chain C: V.6, R.26, S.59 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.26, C:S.59 Water bridges: C:K.23, C:K.23 GOL.9: 3 residues within 4Å: Chain C: K.23, G.24, E.25 1 PLIP interactions: 1 interactions with chain C Water bridges: C:K.23 GOL.10: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain D Water bridges: D:D.10 GOL.11: 4 residues within 4Å: Chain D: D.10, Y.11, E.12, Y.55 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Y.55, D:Y.55

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Calicdan, X. et al., Crystal structure of c-Src SH3 domain in H32 space group mediated by nickel. To Be Published

Release Date

2025-05-14

Peptides

Proto-oncogene tyrosine-protein kinase Src: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Proto-oncogene tyrosine-protein kinase Src