SMTL ID : 6owx.1

Spy H96L:Im7 L18pI-Phe complex; multiple anomalous datasets contained herein for element identification

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.06 Å

Oligo State

homo-dimer

Ligands

13 x ZN: ZINC ION(Non-covalent)

ZN.1: 2 residues within 4Å: Chain A: E.32 Ligands: IMD.15 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.32, A:E.32 ZN.2: 4 residues within 4Å: Chain A: R.35, D.39 Ligands: IMD.12, IMD.17 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.39, A:D.39 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.1 ZN.4: 1 residues within 4Å: Chain A: E.52 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.52 ZN.5: 2 residues within 4Å: Chain A: E.59 Ligands: IMD.13 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.59, A:E.59 ZN.6: 1 residues within 4Å: Chain A: E.71 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.71, H2O.1, H2O.1 ZN.7: 6 residues within 4Å: Chain A: R.35, H.38 Chain B: F.92, E.93 Ligands: CL.11, IMD.17 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.8: 2 residues within 4Å: Chain A: D.9 Ligands: IMD.14 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.9, A:D.9, H2O.1 ZN.9: 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.1 ZN.16: 5 residues within 4Å: Chain A: F.92, E.93 Chain B: R.35, H.38 Ligands: CL.10 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Metal complexes: B:H.38, A:E.93 ZN.18: 2 residues within 4Å: Chain A: K.48 Chain B: E.71 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.71, B:E.71, H2O.2 ZN.19: 2 residues within 4Å: Chain B: R.35, D.39 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.39, B:D.39 ZN.20: 3 residues within 4Å: Chain B: D.47, V.49, K.50 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.47, B:D.47, H2O.1

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

CL.10: 6 residues within 4Å: Chain A: F.92, E.93 Chain B: R.34, R.35, H.38 Ligands: ZN.16 Ligand excluded by PLIP CL.11: 7 residues within 4Å: Chain A: R.34, R.35, H.38 Chain B: F.92, E.93 Ligands: ZN.7, IMD.17 Ligand excluded by PLIP

5 x IMD: IMIDAZOLE(Non-covalent)

IMD.12: 6 residues within 4Å: Chain A: H.38, D.39, A.42 Chain B: N.89 Ligands: ZN.2, IMD.17 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.39 IMD.13: 3 residues within 4Å: Chain A: A.56, E.59 Ligands: ZN.5 No protein-ligand interaction detected (PLIP) IMD.14: 2 residues within 4Å: Chain A: D.9 Ligands: ZN.8 No protein-ligand interaction detected (PLIP) IMD.15: 2 residues within 4Å: Chain A: E.32 Ligands: ZN.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.32 IMD.17: 8 residues within 4Å: Chain A: R.35, H.38, D.39 Chain B: E.93 Ligands: ZN.2, ZN.7, CL.11, IMD.12 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.38

1 x IOD: IODIDE ION(Non-functional Binders)

IOD.21: 3 residues within 4Å: Chain B: F.88, N.91, F.92 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rocchio, S. et al., Identifying dynamic, partially occupied residues using anomalous scattering. Acta Crystallogr D Struct Biol (2019)

Release Date

2019-05-29

Peptides

Periplasmic chaperone Spy: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Periplasmic chaperone Spy

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