SMTL ID : 3ugi.1

Structural and functional characterization of an anesthetic binding site in the second cysteine-rich domain of protein kinase C delta

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.36 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.10, C.40, C.43, C.59 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.10, A:C.40, A:C.43, A:C.59 ZN.2: 4 residues within 4Å: Chain A: C.23, C.26, H.48, C.51 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.23, A:C.26, A:H.48, A:C.51 ZN.6: 4 residues within 4Å: Chain B: H.10, C.40, C.43, C.59 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.10, B:C.40, B:C.43, B:C.59 ZN.7: 4 residues within 4Å: Chain B: C.23, C.26, H.48, C.51 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.23, B:C.26, B:H.48, B:C.51

2 x 09U: (methoxymethyl)cyclopropane(Non-covalent)

09U.3: 6 residues within 4Å: Chain A: Y.15, N.16, Y.17, M.18, S.19 Ligands: PO4.5 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.15, A:M.18 Hydrogen bonds: A:Y.15 09U.8: 5 residues within 4Å: Chain B: Y.15, Y.17, M.18, S.19 Ligands: PO4.10 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Y.15, B:Y.17, B:M.18 Water bridges: B:K.39

6 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.4: 4 residues within 4Å: Chain A: S.9, R.11, D.42 Chain B: R.4 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:D.42 Water bridges: A:S.9, A:S.9, A:R.11, A:D.42, B:S.2 Salt bridges: A:R.11, B:R.4 PO4.5: 4 residues within 4Å: Chain A: K.39, G.44, N.46 Ligands: 09U.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.46 Water bridges: A:K.39, A:K.39 Salt bridges: A:K.39 PO4.9: 4 residues within 4Å: Chain A: R.4 Chain B: S.9, R.11, D.42 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:S.9 Salt bridges: B:R.11, A:R.4 Water bridges: A:R.4, A:R.4 PO4.10: 4 residues within 4Å: Chain B: K.39, G.44, N.46 Ligands: 09U.8 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.46 Water bridges: B:K.39, B:K.39, B:K.39 Salt bridges: B:K.39 PO4.11: 3 residues within 4Å: Chain A: G.1 Chain B: S.9, N.57 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:S.9, B:N.57, A:G.1, A:G.1 Water bridges: B:N.57, A:S.2 PO4.12: 4 residues within 4Å: Chain B: H.10, R.11, F.12, R.52 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:H.10, B:F.12 Water bridges: B:F.12, B:R.52 Salt bridges: B:R.52

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shanmugasundararaj, S. et al., Structural and Functional Characterization of an Anesthetic Binding Site in the Second Cysteine-Rich Domain of Protein Kinase Cdelta. Biophys.J. (2012)

Release Date

2012-12-12

Peptides

Protein kinase C delta type: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Protein kinase C delta type

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