SMTL ID : 7wvg.1

Crystal structure of H18 complexed with SIA28

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

hetero-3-3-3-3-mer

Ligands

3 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.1: 5 residues within 4Å: Chain A: H.8, N.10, N.11 Chain C: G.104, Y.106 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:G.104, C:Y.106, A:N.10, A:N.11 NAG-FUC.6: 5 residues within 4Å: Chain E: H.8, N.10, N.11 Chain G: G.104, Y.106 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain G Hydrogen bonds: E:N.10, G:G.104, G:Y.106, E:N.11 NAG-FUC.11: 5 residues within 4Å: Chain I: H.8, N.10, N.11 Chain K: G.104, Y.106 3 PLIP interactions: 2 interactions with chain K, 1 interactions with chain I Hydrogen bonds: K:G.104, K:Y.106, I:N.10, I:N.11

3 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2: 2 residues within 4Å: Chain A: Q.163, N.236 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 2 residues within 4Å: Chain E: Q.163, N.236 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 2 residues within 4Å: Chain I: Q.163, N.236 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN: 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.3: 8 residues within 4Å: Chain A: K.45, N.259 Chain B: N.56, T.57, Q.58, F.59 Chain D: R.18 Chain I: Q.308 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain I Hydrogen bonds: B:N.56, I:Q.308 NAG-NAG-BMA-MAN-MAN.8: 8 residues within 4Å: Chain A: Q.308 Chain E: K.45, N.259 Chain F: N.56, T.57, Q.58, F.59 Chain H: R.18 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain A Hydrogen bonds: F:N.56, A:Q.308 NAG-NAG-BMA-MAN-MAN.13: 8 residues within 4Å: Chain E: Q.308 Chain I: K.45, N.259 Chain J: N.56, T.57, Q.58, F.59 Chain L: R.18 2 PLIP interactions: 1 interactions with chain J, 1 interactions with chain E Hydrogen bonds: J:N.56, E:Q.308

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

NAG.4: 1 residues within 4Å: Chain B: N.141 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.141 NAG.5: 3 residues within 4Å: Chain B: D.147, N.150, T.152 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.150, B:T.152 NAG.9: 1 residues within 4Å: Chain F: N.141 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:N.141 NAG.10: 3 residues within 4Å: Chain F: D.147, N.150, T.152 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:N.150, F:T.152 NAG.14: 1 residues within 4Å: Chain J: N.141 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:N.141 NAG.15: 3 residues within 4Å: Chain J: D.147, N.150, T.152 2 PLIP interactions: 2 interactions with chain J Hydrogen bonds: J:N.150, J:T.152

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, Y. et al., Structural basis for a human broadly neutralizing influenza A hemagglutinin stem-specific antibody including H17/18 subtypes. Nat Commun (2022)

Release Date

2023-01-18

Peptides

Hemagglutinin: AEI
Hemagglutinin: BFJ
Heavy chain of SIA28: CGK
Light chain of SIA28: DHL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
A

I
A

B
B

F
B

J
B

C
C

G
C

K
C

D
D

H
D

L
D

Hemagglutinin

Hemagglutinin

Heavy chain of SIA28

Light chain of SIA28

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