SMTL ID : 4ezy.1 (3 other biounits)

Crystal structure of the substrate binding domain of E.coli DnaK in complex with the designer peptide NRLILTG

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-tetramer

Ligands

4 x ASN- ARG- LEU- ILE- LEU: synthetic peptide NRLILTG(Non-covalent)

ASN-ARG-LEU-ILE-LEU.1: 14 residues within 4Å: Chain A: T.15, M.16, T.21, F.38, S.39, T.40, A.41, E.42, Q.45, A.47, V.48, T.49, I.50, N.70 19 PLIP interactions: 1 interactions with chain C, 18 interactions with chain A Water bridges: C:Q.150, A:E.14, A:Q.45 Hydrophobic interactions: A:M.16, A:T.21, A:F.38, A:F.38, A:V.48, A:V.48, A:I.50 Hydrogen bonds: A:M.16, A:S.39, A:S.39, A:A.41, A:Q.45, A:T.49, A:T.49, A:N.70 Salt bridges: A:E.42 ASN-ARG-LEU-ILE-LEU.3: 14 residues within 4Å: Chain B: T.15, M.16, T.21, F.38, S.39, T.40, A.41, E.42, Q.45, A.47, V.48, T.49, I.50, N.70 19 PLIP interactions: 18 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:M.16, B:T.21, B:F.38, B:F.38, B:V.48, B:V.48, B:I.50 Hydrogen bonds: B:M.16, B:S.39, B:S.39, B:A.41, B:Q.45, B:T.49, B:T.49, B:N.70 Water bridges: B:E.14, B:Q.45, D:Q.150 Salt bridges: B:E.42 ASN-ARG-LEU-ILE-LEU.5: 14 residues within 4Å: Chain C: T.15, M.16, T.21, F.38, S.39, T.40, A.41, E.42, Q.45, A.47, V.48, T.49, I.50, N.70 20 PLIP interactions: 19 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:M.16, C:T.21, C:F.38, C:F.38, C:V.48, C:V.48, C:I.50 Hydrogen bonds: C:M.16, C:S.39, C:S.39, C:A.41, C:Q.45, C:T.49, C:T.49, C:T.49, C:N.70 Water bridges: C:E.14, C:Q.45, A:Q.150 Salt bridges: C:E.42 ASN-ARG-LEU-ILE-LEU.7: 14 residues within 4Å: Chain D: T.15, M.16, T.21, F.38, S.39, T.40, A.41, E.42, Q.45, A.47, V.48, T.49, I.50, N.70 20 PLIP interactions: 19 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:M.16, D:T.21, D:F.38, D:F.38, D:V.48, D:V.48, D:I.50 Hydrogen bonds: D:M.16, D:S.39, D:S.39, D:A.41, D:Q.45, D:T.49, D:T.49, D:T.49, D:N.70 Water bridges: D:E.14, D:Q.45, B:Q.150 Salt bridges: D:E.42

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

SO4.2: 5 residues within 4Å: Chain A: R.79, H.153, H.156, S.157, K.160 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.79, A:S.157 Water bridges: A:K.160 Salt bridges: A:R.79, A:H.153, A:H.156, A:K.160 SO4.4: 5 residues within 4Å: Chain B: R.79, H.153, H.156, S.157, K.160 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.79, B:S.157 Water bridges: B:K.160 Salt bridges: B:R.79, B:H.153, B:H.156, B:K.160 SO4.6: 5 residues within 4Å: Chain C: R.79, H.153, H.156, S.157, K.160 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:R.79, C:S.157 Water bridges: C:K.160 Salt bridges: C:R.79, C:H.153, C:H.156, C:K.160 SO4.8: 5 residues within 4Å: Chain D: R.79, H.153, H.156, S.157, K.160 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:R.79, D:S.157 Water bridges: D:K.160 Salt bridges: D:R.79, D:H.153, D:H.156, D:K.160

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zahn, M. et al., Structural Studies on the Forward and Reverse Binding Modes of Peptides to the Chaperone DnaK. J.Mol.Biol. (2013)

Release Date

2013-04-17

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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