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

MISREADING CHAPERONE-SUBSTRATE COMPLEXES FROM RANDOM NOISE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.77 Å

Oligo State

homo-dimer

Ligands

13 x ZN: ZINC ION(Non-covalent)

ZN.1: 3 residues within 4Å: Chain A: E.59 Ligands: CL.11, IMD.15 2 PLIP interactions: 2 interactions with chain A Metal complexes: 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 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.52, H2O.4, H2O.4 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: 3 residues within 4Å: Chain A: D.44 Ligands: CL.12, CL.13 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.44, A:D.44 ZN.8: 4 residues within 4Å: Chain A: Q.14, E.17 Chain B: N.6, E.83 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Metal complexes: A:E.17, A:E.17, B:E.83, B:E.83 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: H.69, Q.73, T.97 Ligands: CL.23, CL.24 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.69, B:T.97, B:T.97 ZN.19: 2 residues within 4Å: Chain B: Q.22, H.69 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.69, H2O.6, H2O.8 ZN.20: 3 residues within 4Å: Chain B: D.47, V.49, K.50 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.47, B:D.47, H2O.5, H2O.8, H2O.8 ZN.21: 1 residues within 4Å: Chain B: D.44 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.44, B:D.44, H2O.5, H2O.8, H2O.8

7 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: 3 residues within 4Å: Chain A: E.59 Ligands: ZN.1, IMD.15 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain A: D.44 Ligands: ZN.7, CL.13 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain A: D.44 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.23: 5 residues within 4Å: Chain B: H.69, Q.73, R.95, T.97 Ligands: ZN.18 Ligand excluded by PLIP CL.24: 5 residues within 4Å: Chain B: H.69, Q.73, F.92, T.97 Ligands: ZN.18 Ligand excluded by PLIP

3 x IMD: IMIDAZOLE(Non-covalent)

IMD.15: 4 residues within 4Å: Chain A: A.56, E.59 Ligands: ZN.1, CL.11 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.52, A:E.52 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)

1 x MG: MAGNESIUM ION(Non-covalent)

MG.22: 3 residues within 4Å: Chain B: Q.25, E.71, K.75 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:E.71, H2O.6, H2O.6, H2O.6, H2O.7, H2O.9

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Periplasmic chaperone Spy

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