SMTL ID : 1x27.1

Crystal Structure of Lck SH2-SH3 with SH2 binding site of p130Cas

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-hexamer

Ligands

6 x ASP- PTR- ASP- TYR- VAL: CRK-associated substrate(Non-covalent)

ASP-PTR-ASP-TYR-VAL.1: 16 residues within 4Å: Chain A: R.75, R.95, S.97, E.98, S.99, S.105, K.120, H.121, Y.122, K.123, R.125, I.134, S.135, G.156 Chain E: S.16, H.17 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:K.123, A:K.123 Hydrogen bonds: A:R.75, A:R.75, A:E.98, A:S.99, A:S.105, A:H.121, A:H.121, A:R.125 Salt bridges: A:R.75, A:R.95, A:K.123 ASP-PTR-ASP-TYR-VAL.2: 19 residues within 4Å: Chain B: R.75, R.95, S.97, E.98, S.99, S.105, K.120, H.121, Y.122, K.123, R.125, I.134, S.135, R.137, G.156, C.158 Chain C: S.16, H.17 Chain E: F.111 18 PLIP interactions: 17 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:H.121, B:Y.122, B:K.123 Hydrogen bonds: B:R.75, B:R.75, B:S.97, B:E.98, B:S.99, B:S.105, B:H.121, B:H.121, B:H.121, B:Y.122, B:G.156, C:S.16 Salt bridges: B:R.75, B:R.95 pi-Cation interactions: B:R.75 ASP-PTR-ASP-TYR-VAL.3: 13 residues within 4Å: Chain B: S.16, H.17 Chain C: R.75, R.95, S.97, S.105, K.120, H.121, Y.122, K.123, S.135, R.137, G.156 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:H.121, C:Y.122, C:K.123 Hydrogen bonds: C:R.75, C:S.97, C:S.99, C:S.99, C:S.105, C:H.121, C:H.121, C:H.121, C:G.156 Salt bridges: C:R.75, C:R.95 pi-Cation interactions: C:R.75 ASP-PTR-ASP-TYR-VAL.4: 13 residues within 4Å: Chain D: R.75, R.95, S.97, E.98, S.99, S.105, K.120, H.121, Y.122, K.123, R.125, I.134, G.156 16 PLIP interactions: 16 interactions with chain D Hydrophobic interactions: D:K.120, D:H.121, D:K.123 Hydrogen bonds: D:R.75, D:R.75, D:E.98, D:S.99, D:S.105, D:H.121, D:Y.122, D:R.125, D:R.125 Salt bridges: D:R.75, D:R.95, D:K.120 pi-Cation interactions: D:R.75 ASP-PTR-ASP-TYR-VAL.5: 18 residues within 4Å: Chain A: S.16, H.17 Chain E: R.75, R.95, S.97, E.98, S.99, S.105, K.120, H.121, Y.122, K.123, R.125, I.134, S.135, R.137, G.156, C.158 16 PLIP interactions: 15 interactions with chain E, 1 interactions with chain A Hydrophobic interactions: E:H.121, E:Y.122, E:K.123 Hydrogen bonds: E:S.97, E:E.98, E:E.98, E:S.99, E:S.105, E:H.121, E:H.121, E:Y.122, E:R.125, A:S.16 Salt bridges: E:R.75, E:R.95, E:K.120 ASP-PTR-ASP-TYR-VAL.6: 19 residues within 4Å: Chain B: H.89 Chain D: S.16 Chain F: R.75, R.95, S.97, E.98, S.99, S.105, K.120, H.121, Y.122, K.123, R.125, I.134, S.135, R.137, D.155, G.156, C.158 25 PLIP interactions: 24 interactions with chain F, 1 interactions with chain D Hydrophobic interactions: F:Y.122, F:K.123, F:K.123, F:I.134 Hydrogen bonds: F:R.75, F:R.75, F:E.98, F:E.98, F:S.99, F:S.99, F:S.105, F:S.105, F:H.121, F:H.121, F:H.121, F:R.125, F:R.125, F:R.137, F:G.156, D:S.16 Salt bridges: F:R.75, F:R.95, F:K.120, F:K.123 pi-Cation interactions: F:R.75

6 x NA: SODIUM ION(Non-functional Binders)

NA.7: 3 residues within 4Å: Chain A: E.64, E.66, F.69 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.69 NA.8: 3 residues within 4Å: Chain B: E.64, E.66, F.69 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.64 NA.9: 3 residues within 4Å: Chain C: E.64, E.66, F.69 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:F.69 NA.10: 4 residues within 4Å: Chain D: E.64, P.65, E.66, F.69 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:F.69 NA.11: 4 residues within 4Å: Chain E: E.64, E.66, F.69, F.70 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:E.64 NA.12: 5 residues within 4Å: Chain F: E.64, P.65, E.66, F.69, F.70 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:F.69

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nasertorabi, F. et al., Molecular basis for regulation of Src by the docking protein p130Cas. J.MOL.RECOG. (2006)

Release Date

2006-02-07

Peptides

Proto-oncogene tyrosine-protein kinase LCK: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Proto-oncogene tyrosine-protein kinase LCK