SMTL ID : 6bie.2 (1 other biounit)

MISREADING CHAPERONE-SUBSTRATE COMPLEXES FROM RANDOM NOISE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.77 Å

Oligo State

homo-tetramer

Ligands

26 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: E.59 Chain D: K.48, E.52 Ligands: CL.11, IMD.15 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain A Metal complexes: D:E.52, D:E.52, A:E.59, A:E.59 ZN.2: 2 residues within 4Å: Chain A: H.69, Q.73 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.69, H2O.1, H2O.3, H2O.4 ZN.3: 2 residues within 4Å: Chain A: H.69, Q.73 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.69, H2O.4, H2O.4 ZN.4: 2 residues within 4Å: Chain A: D.39 Ligands: IMD.17 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.39, A:D.39 ZN.5: 2 residues within 4Å: Chain A: K.48, E.52 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.52, H2O.4, H2O.4, H2O.17 ZN.6: 4 residues within 4Å: Chain A: F.92, E.93 Ligands: CL.14, IMD.16 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.93 ZN.7: 5 residues within 4Å: Chain A: D.44 Chain B: D.47, K.50 Ligands: CL.12, CL.13 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Metal complexes: B:D.47, A:D.44, A:D.44 ZN.8: 2 residues within 4Å: Chain A: Q.14, E.17 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.17, A:E.17 ZN.9: 4 residues within 4Å: Chain A: R.35, H.38 Ligands: CL.10, IMD.17 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.38 ZN.18: 5 residues within 4Å: Chain B: E.59 Chain C: K.48, E.52 Ligands: CL.28, IMD.32 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C Metal complexes: B:E.59, B:E.59, C:E.52, C:E.52 ZN.19: 2 residues within 4Å: Chain B: H.69, Q.73 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:H.69, H2O.6, H2O.8, H2O.8 ZN.20: 2 residues within 4Å: Chain B: H.69, Q.73 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.69, H2O.9, H2O.9 ZN.21: 2 residues within 4Å: Chain B: D.39 Ligands: IMD.34 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.39, B:D.39 ZN.22: 2 residues within 4Å: Chain B: K.48, E.52 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.52, H2O.9, H2O.9, H2O.13 ZN.23: 4 residues within 4Å: Chain B: F.92, E.93 Ligands: CL.31, IMD.33 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.93 ZN.24: 5 residues within 4Å: Chain A: D.47, K.50 Chain B: D.44 Ligands: CL.29, CL.30 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Metal complexes: A:D.47, B:D.44, B:D.44 ZN.25: 2 residues within 4Å: Chain B: Q.14, E.17 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.17, B:E.17 ZN.26: 4 residues within 4Å: Chain B: R.35, H.38 Ligands: CL.27, IMD.34 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.38 ZN.35: 5 residues within 4Å: Chain C: H.69, Q.73, T.97 Ligands: CL.40, CL.41 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.69, C:T.97, C:T.97 ZN.36: 2 residues within 4Å: Chain C: Q.22, H.69 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.69, H2O.11, H2O.12 ZN.37: 3 residues within 4Å: Chain C: D.47, V.49, K.50 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.47, C:D.47, H2O.10, H2O.12, H2O.13 ZN.38: 1 residues within 4Å: Chain C: D.44 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.44, C:D.44, H2O.10, H2O.13, H2O.13 ZN.42: 5 residues within 4Å: Chain D: H.69, Q.73, T.97 Ligands: CL.47, CL.48 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.69, D:T.97, D:T.97 ZN.43: 2 residues within 4Å: Chain D: Q.22, H.69 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:H.69, H2O.15, H2O.16 ZN.44: 3 residues within 4Å: Chain D: D.47, V.49, K.50 5 PLIP interactions: 2 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.47, D:D.47, H2O.14, H2O.16, H2O.17 ZN.45: 1 residues within 4Å: Chain D: D.44 5 PLIP interactions: 2 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.44, D:D.44, H2O.14, H2O.16, H2O.17

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

CL.10: 5 residues within 4Å: Chain A: R.34, R.35, H.38 Ligands: ZN.9, IMD.17 Ligand excluded by PLIP CL.11: 5 residues within 4Å: Chain A: E.59 Chain D: K.48, E.52 Ligands: ZN.1, IMD.15 Ligand excluded by PLIP CL.12: 6 residues within 4Å: Chain A: D.44 Chain B: D.47, V.49, K.50 Ligands: ZN.7, CL.13 Ligand excluded by PLIP CL.13: 4 residues within 4Å: Chain A: D.44 Chain B: D.47 Ligands: ZN.7, CL.12 Ligand excluded by PLIP CL.14: 4 residues within 4Å: Chain A: F.92, E.93 Ligands: ZN.6, IMD.16 Ligand excluded by PLIP CL.27: 5 residues within 4Å: Chain B: R.34, R.35, H.38 Ligands: ZN.26, IMD.34 Ligand excluded by PLIP CL.28: 5 residues within 4Å: Chain B: E.59 Chain C: K.48, E.52 Ligands: ZN.18, IMD.32 Ligand excluded by PLIP CL.29: 6 residues within 4Å: Chain A: D.47, V.49, K.50 Chain B: D.44 Ligands: ZN.24, CL.30 Ligand excluded by PLIP CL.30: 4 residues within 4Å: Chain A: D.47 Chain B: D.44 Ligands: ZN.24, CL.29 Ligand excluded by PLIP CL.31: 4 residues within 4Å: Chain B: F.92, E.93 Ligands: ZN.23, IMD.33 Ligand excluded by PLIP CL.40: 5 residues within 4Å: Chain C: H.69, Q.73, R.95, T.97 Ligands: ZN.35 Ligand excluded by PLIP CL.41: 5 residues within 4Å: Chain C: H.69, Q.73, F.92, T.97 Ligands: ZN.35 Ligand excluded by PLIP CL.47: 5 residues within 4Å: Chain D: H.69, Q.73, R.95, T.97 Ligands: ZN.42 Ligand excluded by PLIP CL.48: 5 residues within 4Å: Chain D: H.69, Q.73, F.92, T.97 Ligands: ZN.42 Ligand excluded by PLIP

6 x IMD: IMIDAZOLE(Non-covalent)

IMD.15: 7 residues within 4Å: Chain A: A.56, E.59 Chain D: K.48, V.49, E.52 Ligands: ZN.1, CL.11 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D Water bridges: A:E.52, A:E.52 pi-Cation interactions: D:K.48 IMD.16: 3 residues within 4Å: Chain A: E.93 Ligands: ZN.6, CL.14 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.93 IMD.17: 5 residues within 4Å: Chain A: R.35, H.38 Ligands: ZN.4, ZN.9, CL.10 No protein-ligand interaction detected (PLIP) IMD.32: 7 residues within 4Å: Chain B: A.56, E.59 Chain C: K.48, V.49, E.52 Ligands: ZN.18, CL.28 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:E.52 pi-Cation interactions: C:K.48 Water bridges: B:E.52, B:E.52 IMD.33: 3 residues within 4Å: Chain B: E.93 Ligands: ZN.23, CL.31 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.93 IMD.34: 5 residues within 4Å: Chain B: R.35, H.38 Ligands: ZN.21, ZN.26, CL.27 No protein-ligand interaction detected (PLIP)

2 x MG: MAGNESIUM ION(Non-covalent)

MG.39: 3 residues within 4Å: Chain C: Q.25, E.71, K.75 6 PLIP interactions: 1 interactions with chain C, 5 Ligand-Water interactions Metal complexes: C:E.71, H2O.10, H2O.11, H2O.11, H2O.12, H2O.13 MG.46: 3 residues within 4Å: Chain D: Q.25, E.71, K.75 6 PLIP interactions: 1 interactions with chain D, 5 Ligand-Water interactions Metal complexes: D:E.71, H2O.14, H2O.14, H2O.15, H2O.16, H2O.17

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, J., Misreading chaperone-substrate complexes from random noise. Nat. Struct. Mol. Biol. (2018)

Release Date

2018-10-17

Peptides

Periplasmic chaperone Spy: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
B

D
B

Periplasmic chaperone Spy

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