SMTL ID : 7o6s.1

Crystal structure of a shortened IpgC variant in complex with N-(2H-1,3-benzodioxol-5-ylmethyl)cyclopentanamine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.58 Å

Oligo State

homo-dimer

Ligands

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

CL.1: 4 residues within 4Å: Chain A: A.111, P.112, L.113, K.114 Ligand excluded by PLIP CL.2: 4 residues within 4Å: Chain A: Q.77, F.78, Q.79, Q.80 Ligand excluded by PLIP CL.6: 6 residues within 4Å: Chain B: D.95, Y.96, S.126, N.127, D.128, L.131 Ligand excluded by PLIP

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

DMS.3: 6 residues within 4Å: Chain A: Y.39, A.70, Q.73, I.74, Y.85, H.101 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.104 DMS.4: 6 residues within 4Å: Chain A: Y.36, Y.39, F.51, M.66, G.67, A.70 2 PLIP interactions: 2 interactions with chain A Water bridges: A:G.67 pi-Cation interactions: A:Y.39

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

PEG.5: 6 residues within 4Å: Chain A: T.97, F.100, H.101, K.130, L.131, K.134 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.134 PEG.9: 7 residues within 4Å: Chain B: T.97, F.100, H.101, D.128, K.130, L.131, K.134 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.134

1 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 3 residues within 4Å: Chain B: S.126, N.127, K.132 No protein-ligand interaction detected (PLIP)

1 x 45N: N-(1,3-benzodioxol-5-ylmethyl)cyclopentanamine(Non-covalent)

45N.8: 13 residues within 4Å: Chain A: F.89, N.94, Y.96 Chain B: Y.85, A.86, F.89, P.98, V.99, T.102, K.114, E.117, C.118, L.121 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.89, B:V.99, B:E.117, B:L.121, A:N.94

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gardonyi, M. et al., Crystal structure of a shortened IpgC variant in complex with N-(2H-1,3-benzodioxol-5-ylmethyl)cyclopentanamine. To be published

Release Date

2022-04-20

Peptides

Chaperone protein IpgC: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Chaperone protein IpgC

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