SMTL ID : 7ayw.1

Crystal structure of a shortened IpgC variant in complex with 2H-isoindol-1-amine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.78 Å

Oligo State

homo-dimer

Ligands

2 x F05: 1H-isoindol-3-amine(Non-covalent)

F05.1: 11 residues within 4Å: Chain A: F.89, K.93, N.94, Y.96 Chain B: A.86, F.89, V.99, T.102, E.117, C.118, L.121 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:A.86, B:F.89, B:V.99, B:T.102 Hydrogen bonds: B:E.117, B:E.117 pi-Stacking: B:F.89 F05.8: 4 residues within 4Å: Chain A: Y.60, L.91 Chain B: Q.79, D.83 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:Y.60 Hydrogen bonds: B:Q.79, B:D.83 Water bridges: B:D.83

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

CL.2: 4 residues within 4Å: Chain A: R.43, I.44, E.45, E.46 Ligand excluded by PLIP CL.3: 4 residues within 4Å: Chain A: Q.77, F.78, Q.79, Q.80 Ligand excluded by PLIP CL.4: 2 residues within 4Å: Chain A: P.24, D.25 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain A: K.93 Chain B: Q.79, Q.106, K.114 Ligand excluded by PLIP CL.10: 5 residues within 4Å: Chain B: D.95, Y.96, S.126, D.128, L.131 Ligand excluded by PLIP

1 x MG: MAGNESIUM ION(Non-functional Binders)

MG.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.6: 5 residues within 4Å: Chain A: F.100, H.101, K.130, L.131, K.134 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.134 Water bridges: A:H.101, A:H.101

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.7: 6 residues within 4Å: Chain A: Y.32, Y.36, Y.39, F.51, G.67, A.70 2 PLIP interactions: 2 interactions with chain A pi-Cation interactions: A:Y.36, A:Y.39 DMS.11: 6 residues within 4Å: Chain A: L.121 Chain B: F.89, K.93, N.94, D.95, Y.96 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gardonyi, M. et al., Crystal structure of a shortened IpgC variant in complex with 2H-isoindol-1-amine. To be published

Release Date

2021-11-24

Peptides

Chaperone protein IpgC: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Chaperone protein IpgC

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