SMTL ID : 5wo2.1

Chaperone Spy bound to Casein Fragment (Casein un-modeled)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.77 Å

Oligo State

homo-dimer

Ligands

6 x IMD: IMIDAZOLE(Non-covalent)

IMD.1: 3 residues within 4Å: Chain A: D.47, K.50 Ligands: ZN.11 No protein-ligand interaction detected (PLIP) IMD.2: 4 residues within 4Å: Chain A: A.68, H.69, T.72 Ligands: ZN.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.72 IMD.15: 7 residues within 4Å: Chain A: E.93 Chain B: R.35, H.38, D.39 Ligands: CL.14, ZN.16, IMD.17 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.39, A:E.93 IMD.17: 5 residues within 4Å: Chain A: N.89 Chain B: H.38, D.39, A.42 Ligands: IMD.15 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A pi-Stacking: B:H.38 Hydrogen bonds: A:N.89 IMD.18: 3 residues within 4Å: Chain B: K.48, V.49, E.52 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.52 pi-Cation interactions: B:K.48 IMD.19: 6 residues within 4Å: Chain A: R.34 Chain B: H.69, Q.73, R.95, T.97 Ligands: ZN.20 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.95, B:R.95, B:T.97

16 x ZN: ZINC ION(Non-covalent)

ZN.3: 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.4: 2 residues within 4Å: Chain A: Q.14, E.17 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.17 ZN.5: 3 residues within 4Å: Chain A: H.69, Q.73 Ligands: IMD.2 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.69, H2O.1 ZN.6: 3 residues within 4Å: Chain A: H.69, Q.73 Chain B: M.37 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.69 ZN.7: 2 residues within 4Å: Chain A: E.71, K.75 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.71, A:E.71 ZN.8: 5 residues within 4Å: Chain A: R.35, H.38 Chain B: F.92, E.93 Ligands: CL.9 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Metal complexes: B:E.93, B:E.93, A:H.38 ZN.10: 1 residues within 4Å: Chain A: D.39 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.39, A:D.39 ZN.11: 4 residues within 4Å: Chain A: D.47, V.49, K.50 Ligands: IMD.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.47 ZN.12: 3 residues within 4Å: Chain A: K.48, E.52 Chain B: K.63 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.52, A:E.52 ZN.13: 2 residues within 4Å: Chain A: E.60, K.63 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.60, H2O.3 ZN.16: 6 residues within 4Å: Chain A: F.92, E.93 Chain B: R.35, H.38 Ligands: CL.14, IMD.15 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Metal complexes: B:H.38, A:E.93 ZN.20: 5 residues within 4Å: Chain A: R.34 Chain B: H.69, Q.73, T.97 Ligands: IMD.19 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.69, B:T.97 ZN.21: 1 residues within 4Å: Chain B: E.71 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.71 ZN.22: 1 residues within 4Å: Chain B: D.44 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.44, B:D.44 ZN.23: 1 residues within 4Å: Chain B: H.69 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.69 ZN.24: 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

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

CL.9: 6 residues within 4Å: Chain A: R.34, R.35, H.38 Chain B: F.92, E.93 Ligands: ZN.8 Ligand excluded by PLIP CL.14: 7 residues within 4Å: Chain A: F.92, E.93 Chain B: R.34, R.35, H.38 Ligands: IMD.15, ZN.16 Ligand excluded by PLIP

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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