SMTL ID : 4ezs.1 (4 other biounits)

Crystal structure of the substrate binding domain of E.coli DnaK in complex with metchnikowin (residues 20 to 26)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-tetramer

Ligands

4 x PRO- ARG- PRO- GLY- PRO- ILE- TYR- TYR: Metchnikowin(Non-covalent)

PRO-ARG-PRO-GLY-PRO-ILE-TYR-TYR.1: 23 residues within 4Å: Chain A: E.14, T.15, M.16, G.17, G.18, V.37, F.38, S.39, A.41, Q.45, A.47, V.48, T.49, R.79, G.80, M.81, P.82, H.153 Chain C: Q.150, H.153, L.154, S.157 Ligands: PRO-ARG-PRO-GLY-PRO-ILE-TYR-TYR.5 18 PLIP interactions: 14 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:V.37, A:F.38, C:Q.150 Hydrogen bonds: A:M.16, A:G.17, A:G.18, A:S.39, A:S.39, A:A.41, A:Q.45, A:T.49, A:T.49, A:G.80, A:H.153, C:S.157, C:S.157 Salt bridges: A:E.14 Water bridges: C:S.157 PRO-ARG-PRO-GLY-PRO-ILE-TYR-TYR.3: 23 residues within 4Å: Chain B: E.14, T.15, M.16, G.17, G.18, V.37, F.38, S.39, A.41, Q.45, A.47, V.48, T.49, R.79, G.80, M.81, P.82, H.153 Chain D: Q.150, H.153, L.154, S.157 Ligands: PRO-ARG-PRO-GLY-PRO-ILE-TYR-TYR.7 18 PLIP interactions: 14 interactions with chain B, 4 interactions with chain D Hydrophobic interactions: B:V.37, B:F.38, D:Q.150 Hydrogen bonds: B:M.16, B:G.17, B:G.18, B:S.39, B:S.39, B:A.41, B:Q.45, B:T.49, B:T.49, B:G.80, B:H.153, D:S.157, D:S.157 Salt bridges: B:E.14 Water bridges: D:S.157 PRO-ARG-PRO-GLY-PRO-ILE-TYR-TYR.5: 23 residues within 4Å: Chain A: Q.150, H.153, L.154, S.157 Chain C: E.14, T.15, M.16, G.17, G.18, V.37, F.38, S.39, A.41, Q.45, A.47, V.48, T.49, R.79, G.80, M.81, P.82, H.153 Ligands: PRO-ARG-PRO-GLY-PRO-ILE-TYR-TYR.1 19 PLIP interactions: 4 interactions with chain A, 15 interactions with chain C Hydrophobic interactions: A:Q.150, C:V.37, C:F.38 Hydrogen bonds: A:S.157, A:S.157, C:M.16, C:G.17, C:G.18, C:S.39, C:S.39, C:A.41, C:Q.45, C:A.47, C:T.49, C:T.49, C:G.80, C:H.153 Water bridges: A:S.157 Salt bridges: C:E.14 PRO-ARG-PRO-GLY-PRO-ILE-TYR-TYR.7: 23 residues within 4Å: Chain B: Q.150, H.153, L.154, S.157 Chain D: E.14, T.15, M.16, G.17, G.18, V.37, F.38, S.39, A.41, Q.45, A.47, V.48, T.49, R.79, G.80, M.81, P.82, H.153 Ligands: PRO-ARG-PRO-GLY-PRO-ILE-TYR-TYR.3 19 PLIP interactions: 15 interactions with chain D, 4 interactions with chain B Hydrophobic interactions: D:V.37, D:F.38, B:Q.150 Hydrogen bonds: D:M.16, D:G.17, D:G.18, D:S.39, D:S.39, D:A.41, D:Q.45, D:A.47, D:T.49, D:T.49, D:G.80, D:H.153, B:S.157, B:S.157 Salt bridges: D:E.14 Water bridges: B:S.157

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 2 residues within 4Å: Chain A: R.57, N.134 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.134 Water bridges: A:R.57 Salt bridges: A:R.57 SO4.4: 2 residues within 4Å: Chain B: R.57, N.134 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.134 Water bridges: B:R.57 Salt bridges: B:R.57 SO4.6: 2 residues within 4Å: Chain C: R.57, N.134 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.134 Water bridges: C:R.57 Salt bridges: C:R.57 SO4.8: 2 residues within 4Å: Chain D: R.57, N.134 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.134 Water bridges: D:R.57 Salt bridges: D:R.57

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zahn, M. et al., Structural studies of DnaK in complex with proline rich antimicrobial peptides reveal two different peptide binding modes. To be Published

Release Date

2013-04-24

Peptides

Chaperone protein DnaK: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Chaperone protein DnaK

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