SMTL ID : 5wo3.1

Chaperone Spy bound to Im7 (Im7 un-modeled)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.87 Å

Oligo State

homo-dimer

Ligands

12 x ZN: ZINC ION(Non-covalent)(Non-functional Binders)

ZN.1: 6 residues within 4Å: Chain A: F.92, E.93 Chain B: R.35, H.38 Ligands: CL.5, IMD.10 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Metal complexes: B:H.38, A:E.93 ZN.2: 1 residues within 4Å: Chain A: E.59 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.59, A:E.59 ZN.3: 1 residues within 4Å: Chain A: D.44 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.44, A:D.44, H2O.3 ZN.4: 2 residues within 4Å: Chain A: Q.14, E.17 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.17, H2O.1 ZN.7: 3 residues within 4Å: Chain A: M.70, Q.73 Chain B: I.41 No protein-ligand interaction detected (PLIP) ZN.8: 2 residues within 4Å: Ligands: CL.6, IMD.12 No protein-ligand interaction detected (PLIP) ZN.9: 1 residues within 4Å: Chain A: R.35 No protein-ligand interaction detected (PLIP) ZN.13: 3 residues within 4Å: Chain B: D.39 Ligands: IMD.10, IMD.12 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.39, B:D.39 ZN.14: 2 residues within 4Å: Chain B: E.60, K.63 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.60, B:E.60 ZN.15: 2 residues within 4Å: Chain B: Q.13, E.17 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.17 ZN.16: 1 residues within 4Å: Chain B: D.44 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.44, B:D.44, H2O.7 ZN.17: 2 residues within 4Å: Chain B: V.49 Ligands: IMD.11 No protein-ligand interaction detected (PLIP)

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 7 residues within 4Å: Chain A: F.92, E.93 Chain B: R.34, R.35, H.38 Ligands: ZN.1, IMD.10 Ligand excluded by PLIP CL.6: 2 residues within 4Å: Ligands: ZN.8, IMD.12 Ligand excluded by PLIP

3 x IMD: IMIDAZOLE(Non-covalent)

IMD.10: 8 residues within 4Å: Chain A: E.93 Chain B: R.35, H.38, D.39 Ligands: ZN.1, CL.5, IMD.12, ZN.13 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.35 pi-Cation interactions: B:R.35 IMD.11: 4 residues within 4Å: Chain B: K.48, V.49, E.52 Ligands: ZN.17 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.48 Water bridges: B:E.52 IMD.12: 8 residues within 4Å: Chain A: N.89 Chain B: H.38, D.39, A.42 Ligands: CL.6, ZN.8, IMD.10, ZN.13 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.39

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Horowitz, S. et al., Visualizing chaperone-assisted protein folding. Nat. Struct. Mol. Biol. (2016)

Release Date

2017-08-16

Peptides

Periplasmic chaperone Spy: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Periplasmic chaperone Spy

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