SMTL ID : 8r3b.1

Cocrystal form I of the Pent - sulfonato-calix[8]arene complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.66 Å

Oligo State

homo-pentamer

Ligands

1 x EVB: sulfonato-calix[8]arene(Non-covalent)

EVB.1: 12 residues within 4Å: Chain A: F.4, K.5 Chain B: F.4, K.5 Chain C: F.4, K.5 Chain D: S.2, F.4, K.5 Chain E: G.3, F.4, K.5 19 PLIP interactions: 3 interactions with chain B, 6 interactions with chain E, 2 interactions with chain C, 3 interactions with chain A, 5 interactions with chain D Hydrophobic interactions: B:K.5, E:K.5, E:K.5, C:K.5, A:K.5, D:K.5, D:K.5 Hydrogen bonds: B:K.5, E:G.3 Water bridges: B:K.5, E:F.4, E:D.21, A:K.5, D:K.5, D:N.20 Salt bridges: E:K.5, C:K.5, A:K.5, D:K.5

5 x NDG: 2-acetamido-2-deoxy-alpha-D-glucopyranose(Non-covalent)

NDG.2: 12 residues within 4Å: Chain A: G.44, N.45, G.46, G.47, W.48 Chain C: F.4, D.32, K.33, D.34, N.35, W.36, L.37 11 PLIP interactions: 7 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:W.48, C:F.4 Hydrogen bonds: A:N.45, A:G.46, A:G.46, A:G.46, A:W.48, C:W.36, C:L.37 Water bridges: A:I.43, C:D.34 NDG.3: 11 residues within 4Å: Chain A: F.4, D.32, D.34, N.35, W.36, L.37 Chain B: G.44, N.45, G.46, G.47, W.48 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:W.48, A:F.4 Hydrogen bonds: B:N.45, B:G.46, B:G.46, B:W.48, A:W.36, A:L.37 Water bridges: A:N.35 NDG.4: 12 residues within 4Å: Chain C: G.44, N.45, G.46, G.47, W.48 Chain D: F.4, D.32, K.33, D.34, N.35, W.36, L.37 9 PLIP interactions: 6 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:W.48, D:F.4 Hydrogen bonds: C:N.45, C:G.46, C:G.46, C:G.46, C:W.48, D:W.36, D:L.37 NDG.5: 11 residues within 4Å: Chain D: G.44, N.45, G.46, G.47, W.48 Chain E: F.4, D.32, D.34, N.35, W.36, L.37 11 PLIP interactions: 7 interactions with chain D, 4 interactions with chain E Hydrophobic interactions: D:W.48, E:F.4 Hydrogen bonds: D:N.45, D:G.46, D:G.46, D:G.46, D:W.48, E:W.36, E:L.37 Water bridges: D:I.43, E:S.31 NDG.6: 12 residues within 4Å: Chain B: F.4, D.32, K.33, D.34, N.35, W.36, L.37 Chain E: G.44, N.45, G.46, G.47, W.48 10 PLIP interactions: 4 interactions with chain B, 6 interactions with chain E Hydrophobic interactions: B:F.4, E:W.48 Hydrogen bonds: B:K.33, B:W.36, B:L.37, E:N.45, E:G.46, E:G.46, E:G.46, E:W.48

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Flood, R.J. et al., Multivalent Calixarene Complexation of a Designed Pentameric Lectin. Biomacromolecules (2024)

Release Date

2024-03-06

Peptides

Beta propeller: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
E

D
D

E
C

Beta propeller

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