SMTL ID : 6b3m.2 (1 other biounit)

The crystal structure of a broadly-reactive human anti-hemagglutinin stalk antibody (70-1F02) in complex with H5 hemagglutinin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.92 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: 3 residues within 4Å: Chain A: N.165, N.236, A.238 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain D: N.165, N.236, A.238 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain E: E.147, E.150, N.154, T.156 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG- MAN- MAN- BMA: alpha-D-mannopyranose-(1-3)-[beta-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-BMA.2: 9 residues within 4Å: Chain A: K.36, N.38, N.286 Chain C: V.5, S.21, R.23, T.76, Y.80 Ligands: NAG-NAG-MAN-BMA.3 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.23, C:Y.80 NAG-NAG-MAN-MAN-BMA.4: 11 residues within 4Å: Chain D: K.36, N.286 Chain F: V.5, Q.6, S.7, K.19, S.21, R.23, D.73, T.76, Y.80 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:Q.6, F:R.23, F:K.19, F:K.19

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

NAG-NAG-MAN-BMA.3: 5 residues within 4Å: Chain A: N.11 Chain C: K.19, T.71, E.82 Ligands: NAG-NAG-MAN-MAN-BMA.2 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.19, C:T.71, C:E.82

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

NAG.7: 1 residues within 4Å: Chain A: N.23 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.15, A:N.23 NAG.8: 3 residues within 4Å: Chain B: E.150, N.154, T.156 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.150, B:N.154, B:T.156 NAG.9: 1 residues within 4Å: Chain D: N.11 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.11 NAG.12: 2 residues within 4Å: Chain I: Q.15, N.23 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:Q.15, I:N.23

2 x NAG- NAG- MAN- MAN: alpha-D-mannopyranose-(1-3)-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.10: 7 residues within 4Å: Chain I: K.36, H.37, N.38, N.286 Chain K: K.19, R.23, Y.80 2 PLIP interactions: 2 interactions with chain K Hydrogen bonds: K:K.19, K:Y.80 NAG-NAG-MAN-MAN.11: 2 residues within 4Å: Chain I: N.165, A.238 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nachbagauer, R. et al., Broadly Reactive Human Monoclonal Antibodies Elicited following Pandemic H1N1 Influenza Virus Exposure Protect Mice against Highly Pathogenic H5N1 Challenge. J. Virol. (2018)

Release Date

2018-06-13

Peptides

Hemagglutinin HA1: ADI
Hemagglutinin HA2: BEJ
70-1F02 Fab Heavy Chain: CFK
70-1F02 Fab Light Chain: GHL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

D
Q

I
S

B
F

E
R

J
T

C
M

F
Y

K
V

G
U

H
N

L
W

Hemagglutinin HA1

Hemagglutinin HA2

70-1F02 Fab Heavy Chain

70-1F02 Fab Light Chain

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