SMTL ID : 7shz.1 (1 other biounit)

IgE-Fc in complex with HAE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

hetero-2-2-2-mer

Ligands

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN-MAN.1: 13 residues within 4Å: Chain A: Y.41, S.43, R.44, L.61, V.63, D.64, Q.94, N.96, T.98, I.176, T.194, Q.196 Chain D: R.198 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.196, A:Y.41, A:Y.41

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.2: 10 residues within 4Å: Chain D: Y.41, S.43, V.63, Q.94, N.96, T.98, T.100, Q.196 Ligands: MAN.8, MAN.9 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:S.43, D:Q.196, D:Q.196, D:Y.41

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.3: 2 residues within 4Å: Chain A: N.73, T.75 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.73

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.4: 3 residues within 4Å: Chain B: S.72, R.73, Q.83 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.72, B:S.72, B:Q.83 PO4.5: 2 residues within 4Å: Chain B: L.47, E.48 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.45, B:E.48

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.6: 6 residues within 4Å: Chain B: N.37, W.49, S.52, K.60 Chain C: D.101, Y.103 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:W.49, B:K.60, C:Y.103 Hydrogen bonds: B:S.52 Salt bridges: B:K.60

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.7: 5 residues within 4Å: Chain C: Q.44, K.52, L.54, P.66, F.69 No protein-ligand interaction detected (PLIP) EDO.11: 9 residues within 4Å: Chain A: A.79, T.117, Q.119 Chain E: S.101, H.102, H.108 Chain F: Y.56, E.62, S.63 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:H.108

2 x MAN: alpha-D-mannopyranose(Non-functional Binders)(Non-covalent)

MAN.8: 2 residues within 4Å: Ligands: NAG-NAG-BMA-MAN.2, NAG-NAG-BMA-MAN.2 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Y.41, D:Y.41 MAN.9: 5 residues within 4Å: Chain A: R.198 Chain D: T.194, Q.196 Ligands: NAG-NAG-BMA-MAN.2, NAG-NAG-BMA-MAN.2 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:Q.196, A:R.198

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 3 residues within 4Å: Chain D: D.222, S.244, V.245 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pennington, L.F. et al., Directed evolution of and structural insights into antibody-mediated disruption of a stable receptor-ligand complex. Nat Commun (2021)

Release Date

2021-12-22

Peptides

IgE Fc: AD
HAE Variable fragment Heavy chain: BE
HAE Variable fragment Light chain: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

D
A

B
C

E
E

C
D

F
F

IgE Fc

HAE Variable fragment Heavy chain

HAE Variable fragment Light chain

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