SMTL ID : 5w42.1

Crystal structure of human monoclonal antibody H3v-47 in complex with influenza virus hemagglutinin from A/Minnesota/11/2010 (H3N2)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.57 Å

Oligo State

hetero-3-3-3-3-mer

Ligands

6 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.1: 2 residues within 4Å: Chain A: N.38, A.39 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.5: 2 residues within 4Å: Chain A: N.63, Y.94 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.10: 2 residues within 4Å: Chain E: N.38, A.39 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.14: 2 residues within 4Å: Chain E: N.63, Y.94 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.19: 2 residues within 4Å: Chain I: N.38, A.39 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.23: 2 residues within 4Å: Chain I: N.63, Y.94 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-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: 7 residues within 4Å: Chain A: E.163, N.165, R.201, N.246, S.247, T.248 Ligands: NAG-NAG-MAN-MAN-MAN-MAN.3 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain E Hydrogen bonds: A:E.163, A:E.163, E:D.188 NAG-NAG-BMA-MAN.11: 7 residues within 4Å: Chain E: E.163, N.165, R.201, N.246, S.247, T.248 Ligands: NAG-NAG-MAN-MAN-MAN-MAN.12 4 PLIP interactions: 2 interactions with chain I, 2 interactions with chain E Hydrogen bonds: I:D.188, I:D.188, E:E.163, E:E.163 NAG-NAG-BMA-MAN.20: 7 residues within 4Å: Chain I: E.163, N.165, R.201, N.246, S.247, T.248 Ligands: NAG-NAG-MAN-MAN-MAN-MAN.21 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain I Hydrogen bonds: A:D.188, I:E.163

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

NAG-NAG-MAN-MAN-MAN-MAN.3: 7 residues within 4Å: Chain A: N.165, T.167 Chain E: Y.137, S.219, W.222, S.227 Ligands: NAG-NAG-BMA-MAN.2 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:W.222, E:S.227 NAG-NAG-MAN-MAN-MAN-MAN.12: 7 residues within 4Å: Chain E: N.165, T.167 Chain I: Y.137, S.219, W.222, S.227 Ligands: NAG-NAG-BMA-MAN.11 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:W.222, I:S.227 NAG-NAG-MAN-MAN-MAN-MAN.21: 7 residues within 4Å: Chain A: Y.137, S.219, W.222, S.227 Chain I: N.165, T.167 Ligands: NAG-NAG-BMA-MAN.20 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.222, A:S.227

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

NAG-NAG-BMA.4: 3 residues within 4Å: Chain A: N.285, V.297, N.298 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.13: 3 residues within 4Å: Chain E: N.285, V.297, N.298 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.22: 3 residues within 4Å: Chain I: N.285, V.297, N.298 No protein-ligand interaction detected (PLIP)

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.6: 2 residues within 4Å: Chain B: G.150, N.154 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 2 residues within 4Å: Chain F: G.150, N.154 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 2 residues within 4Å: Chain J: G.150, N.154 No protein-ligand interaction detected (PLIP)

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

NAG.7: 3 residues within 4Å: Chain A: V.20, N.22, T.24 No protein-ligand interaction detected (PLIP) NAG.8: 1 residues within 4Å: Chain A: N.126 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.126, A:T.128 NAG.16: 3 residues within 4Å: Chain E: V.20, N.22, T.24 No protein-ligand interaction detected (PLIP) NAG.17: 1 residues within 4Å: Chain E: N.126 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.126, E:T.128 NAG.25: 3 residues within 4Å: Chain I: V.20, N.22, T.24 No protein-ligand interaction detected (PLIP) NAG.26: 1 residues within 4Å: Chain I: N.126 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:N.126, I:T.128

3 x ZN: ZINC ION(Non-covalent)

ZN.9: 2 residues within 4Å: Chain C: C.230, H.232 No protein-ligand interaction detected (PLIP) ZN.18: 2 residues within 4Å: Chain G: C.230, H.232 No protein-ligand interaction detected (PLIP) ZN.27: 2 residues within 4Å: Chain K: C.230, H.232 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bangaru, S. et al., A multifunctional human monoclonal neutralizing antibody that targets a unique conserved epitope on influenza HA. Nat Commun (2018)

Release Date

2018-07-25

Peptides

Hemagglutinin: AEI
Hemagglutinin: BFJ
Fab H3v-47 heavy chain: CGK
Fab H3v-47 light chain: DHL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
A

I
A

B
B

F
B

J
B

C
H

G
H

K
H

D
L

H
L

L
L

Hemagglutinin

Hemagglutinin

Fab H3v-47 heavy chain

Fab H3v-47 light chain

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