SMTL ID : 4py8.1

Crystal structure of Fab 3.1 in complex with the 1918 influenza virus hemagglutinin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.91 Å

Oligo State

hetero-3-3-3-3-mer

Ligands

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.1: 6 residues within 4Å: Chain A: N.68, E.70, E.90, N.91, C.94, R.225 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 6 residues within 4Å: Chain E: N.68, E.70, E.90, N.91, C.94, R.225 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 6 residues within 4Å: Chain I: N.68, E.70, E.90, N.91, C.94, R.225 No protein-ligand interaction detected (PLIP)

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

NAG.2: 1 residues within 4Å: Chain A: N.27 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.27 NAG.3: 2 residues within 4Å: Chain A: N.280, N.291 No protein-ligand interaction detected (PLIP) NAG.7: 1 residues within 4Å: Chain E: N.27 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.27 NAG.8: 2 residues within 4Å: Chain E: N.280, N.291 No protein-ligand interaction detected (PLIP) NAG.12: 1 residues within 4Å: Chain I: N.27 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:N.27 NAG.13: 2 residues within 4Å: Chain I: N.280, N.291 No protein-ligand interaction detected (PLIP)

6 x MLI: MALONATE ION(Non-functional Binders)

MLI.4: 8 residues within 4Å: Chain B: Q.38 Chain C: R.106, I.108 Chain D: W.32, Y.49, A.50, A.91 Ligands: MLI.5 7 PLIP interactions: 3 interactions with chain C, 3 interactions with chain D, 1 interactions with chain B Hydrogen bonds: C:R.106, D:A.50, B:Q.38 Salt bridges: C:R.106, C:R.106 Hydrophobic interactions: D:W.32, D:A.91 MLI.5: 6 residues within 4Å: Chain C: I.105, R.106 Chain D: A.91, N.92, F.94 Ligands: MLI.4 No protein-ligand interaction detected (PLIP) MLI.9: 8 residues within 4Å: Chain F: Q.38 Chain G: R.106, I.108 Chain H: W.32, Y.49, A.50, A.91 Ligands: MLI.10 7 PLIP interactions: 1 interactions with chain F, 3 interactions with chain H, 3 interactions with chain G Hydrogen bonds: F:Q.38, H:A.50, G:R.106 Hydrophobic interactions: H:W.32, H:A.91 Salt bridges: G:R.106, G:R.106 MLI.10: 6 residues within 4Å: Chain G: I.105, R.106 Chain H: A.91, N.92, F.94 Ligands: MLI.9 No protein-ligand interaction detected (PLIP) MLI.14: 8 residues within 4Å: Chain J: Q.38 Chain K: R.106, I.108 Chain L: W.32, Y.49, A.50, A.91 Ligands: MLI.15 7 PLIP interactions: 1 interactions with chain J, 3 interactions with chain L, 3 interactions with chain K Hydrogen bonds: J:Q.38, L:A.50, K:R.106 Hydrophobic interactions: L:W.32, L:A.91 Salt bridges: K:R.106, K:R.106 MLI.15: 6 residues within 4Å: Chain K: I.105, R.106 Chain L: A.91, N.92, F.94 Ligands: MLI.14 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wyrzucki, A. et al., Alternative Recognition of the Conserved Stem Epitope in Influenza A Virus Hemagglutinin by a VH3-30-Encoded Heterosubtypic Antibody. J.Virol. (2014)

Release Date

2014-05-21

Peptides

Hemagglutinin HA1 chain: AEI
Hemagglutinin HA2 chain: BFJ
antibody 3.1 heavy chain: CGK
antibody 3.1 light chain: DHL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
A

I
A

B
B

F
B

J
B

C
I

G
I

K
I

D
J

H
J

L
J

Hemagglutinin HA1 chain

Hemagglutinin HA2 chain

antibody 3.1 heavy chain

antibody 3.1 light chain

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