SMTL ID : 4u5w.1

Crystal Structure of HIV-1 Nef-SF2 Core Domain in Complex with the Src Family Kinase Hck SH3-SH2 Tandem Regulatory Domains

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.86 Å

Oligo State

hetero-2-2-mer

Ligands

3 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.1: 4 residues within 4Å: Chain A: R.21 Chain B: H.23, D.26, Y.57 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.21 Hydrophobic interactions: B:Y.57, B:Y.57 MPD.2: 5 residues within 4Å: Chain A: Q.17, V.18, P.19 Chain B: N.61 Chain D: E.151 7 PLIP interactions: 1 interactions with chain B, 3 interactions with chain D, 3 interactions with chain A Hydrophobic interactions: B:N.61, A:Q.17, A:Q.17, A:P.19 Hydrogen bonds: D:E.151 Water bridges: D:E.151, D:E.151 MPD.3: 8 residues within 4Å: Chain A: L.41, L.44, R.50, I.53, L.54 Chain C: L.44, R.50, L.54 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:L.41, A:L.44, A:R.50, A:I.53, C:L.44, C:L.54 Hydrogen bonds: A:L.54

6 x IOD: IODIDE ION(Non-functional Binders)

IOD.4: 4 residues within 4Å: Chain A: R.21, P.22 Chain D: T.145 Ligands: IOD.9 Ligand excluded by PLIP IOD.5: 2 residues within 4Å: Chain B: L.69, Q.150 Ligand excluded by PLIP IOD.6: 2 residues within 4Å: Chain B: W.74, P.170 Ligand excluded by PLIP IOD.7: 3 residues within 4Å: Chain C: L.20, R.21, P.22 Ligand excluded by PLIP IOD.8: 3 residues within 4Å: Chain D: W.74, K.157, P.170 Ligand excluded by PLIP IOD.9: 3 residues within 4Å: Chain D: L.133, N.135 Ligands: IOD.4 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Alvarado, J.J. et al., Interaction with the Src Homology (SH3-SH2) Region of the Src-family Kinase Hck Structures the HIV-1 Nef Dimer for Kinase Activation and Effector Recruitment. J.Biol.Chem. (2014)

Release Date

2014-08-20

Peptides

Protein Nef: AC
Tyrosine-protein kinase HCK: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

Protein Nef

Tyrosine-protein kinase HCK