SMTL ID : 5wo1.1

Chaperone Spy H96L bound to Im7 L18A L19A L37A (Im7 un-modeled)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.87 Å

Oligo State

homo-dimer

Ligands

5 x IMD: IMIDAZOLE(Non-covalent)

IMD.1: 9 residues within 4Å: Chain A: E.93 Chain B: R.35, H.38, D.39 Ligands: ZN.2, CL.6, ZN.23, ZN.24, ZN.33 1 PLIP interactions: 1 interactions with chain B pi-Cation interactions: B:R.35 IMD.17: 5 residues within 4Å: Chain B: K.48, V.49, E.52 Ligands: ZN.21, ZN.28 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.52 IMD.18: 8 residues within 4Å: Chain A: R.35, H.38, D.39 Chain B: E.93 Ligands: CL.5, ZN.11, ZN.15, IMD.19 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.38 IMD.19: 8 residues within 4Å: Chain A: R.35, H.38, D.39 Chain B: F.92, E.93 Ligands: CL.5, ZN.15, IMD.18 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.38 IMD.20: 9 residues within 4Å: Chain B: D.4, L.5, N.6, E.83, Q.84, Q.87 Ligands: ZN.26, ZN.27, ZN.35 2 PLIP interactions: 2 interactions with chain B Water bridges: B:L.5, B:N.6

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

ZN.2: 6 residues within 4Å: Chain A: F.92, E.93 Chain B: R.35, H.38 Ligands: IMD.1, CL.6 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Metal complexes: B:H.38, A:E.93 ZN.3: 4 residues within 4Å: Chain A: D.47, K.50 Ligands: ZN.4, GLU.14 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Ligand interactions Metal complexes: A:D.47, A:D.47, GLU.14, GLU.14 ZN.4: 5 residues within 4Å: Chain A: D.47, V.49, K.50 Ligands: ZN.3, GLU.14 No protein-ligand interaction detected (PLIP) ZN.7: 1 residues within 4Å: Chain A: K.63 No protein-ligand interaction detected (PLIP) ZN.8: 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.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) ZN.10: 1 residues within 4Å: Chain A: E.60 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.60 ZN.11: 2 residues within 4Å: Chain A: R.35 Ligands: IMD.18 No protein-ligand interaction detected (PLIP) ZN.12: 2 residues within 4Å: Chain A: Q.14, I.79 No protein-ligand interaction detected (PLIP) ZN.13: 2 residues within 4Å: Chain A: E.83, K.86 No protein-ligand interaction detected (PLIP) ZN.15: 7 residues within 4Å: Chain A: R.35, H.38 Chain B: F.92, E.93 Ligands: CL.5, IMD.18, IMD.19 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Metal complexes: A:H.38, B:E.93, B:E.93 ZN.16: 1 residues within 4Å: Chain A: D.9 No protein-ligand interaction detected (PLIP) ZN.21: 4 residues within 4Å: Chain A: K.63 Chain B: E.52 Ligands: IMD.17, ZN.28 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.52, B:E.52 ZN.22: 2 residues within 4Å: Chain B: D.47, K.50 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.47, B:D.47, H2O.4 ZN.23: 6 residues within 4Å: Chain B: R.35, A.36, H.38, D.39 Ligands: IMD.1, ZN.33 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:R.35, B:D.39, B:D.39 ZN.24: 3 residues within 4Å: Chain B: D.39 Ligands: IMD.1, ZN.33 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.39 ZN.25: 1 residues within 4Å: Chain B: E.17 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.17 ZN.26: 3 residues within 4Å: Chain B: Q.87 Ligands: IMD.20, ZN.30 No protein-ligand interaction detected (PLIP) ZN.27: 2 residues within 4Å: Chain B: N.6 Ligands: IMD.20 No protein-ligand interaction detected (PLIP) ZN.28: 4 residues within 4Å: Chain A: K.63 Chain B: E.52 Ligands: IMD.17, ZN.21 No protein-ligand interaction detected (PLIP) ZN.29: 3 residues within 4Å: Chain B: D.39, A.42, S.43 No protein-ligand interaction detected (PLIP) ZN.30: 4 residues within 4Å: Chain B: E.83, K.86, Q.87 Ligands: ZN.26 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.83 ZN.31: 2 residues within 4Å: Chain B: E.71 Ligands: ZN.32 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.71 ZN.32: 1 residues within 4Å: Ligands: ZN.31 No protein-ligand interaction detected (PLIP) ZN.33: 5 residues within 4Å: Chain B: R.35, D.39 Ligands: IMD.1, ZN.23, ZN.24 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.39, B:D.39 ZN.34: 2 residues within 4Å: Chain B: K.57, E.60 No protein-ligand interaction detected (PLIP) ZN.35: 2 residues within 4Å: Chain B: N.6 Ligands: IMD.20 No protein-ligand interaction detected (PLIP)

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

CL.5: 8 residues within 4Å: Chain A: R.34, R.35, H.38 Chain B: F.92, E.93 Ligands: ZN.15, IMD.18, IMD.19 Ligand excluded by PLIP CL.6: 7 residues within 4Å: Chain A: F.92, E.93 Chain B: R.34, R.35, H.38 Ligands: IMD.1, ZN.2 Ligand excluded by PLIP

1 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.14: 5 residues within 4Å: Chain A: S.43, D.47, K.50 Ligands: ZN.3, ZN.4 7 PLIP interactions: 3 interactions with chain A, 4 Ligand-Ligand interactions Hydrogen bonds: A:K.50, E.14, E.14, E.14, E.14 Water bridges: A:D.47 Salt bridges: A:K.50

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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