SMTL ID : 6b3m.1 (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

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.1: 10 residues within 4Å: Chain A: N.286, S.288 Chain C: V.5, Q.6, S.7, G.8, S.21, R.23, Y.80 Ligands: BMA.12 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.6, C:R.23 NAG-NAG-MAN-MAN.10: 7 residues within 4Å: Chain D: K.36, N.38, A.284, N.286 Chain I: S.21, R.23, Y.80 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:Y.80, I:R.23

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

NAG-NAG-MAN.2: 5 residues within 4Å: Chain A: N.165, N.166, P.235, N.236, D.237 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.3: 2 residues within 4Å: Chain A: Q.15, N.23 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 6 residues within 4Å: Chain B: E.147, E.150, S.151, N.154, T.156 Chain L: S.31 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:E.147 NAG-NAG.5: 5 residues within 4Å: Chain D: N.165, N.236, D.237, A.238 Chain G: S.217 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 1 residues within 4Å: Chain D: N.11 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 2 residues within 4Å: Chain G: N.154, T.156 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain G: N.165, N.236, A.238 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- MAN- MAN- MAN: 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.8: 11 residues within 4Å: Chain F: V.5, Q.6, S.7, K.19, S.21, R.23, Y.80 Chain G: K.36, H.37, N.38, N.286 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:Q.6, F:R.23

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

NAG.11: 1 residues within 4Å: Chain A: N.11 No protein-ligand interaction detected (PLIP) NAG.13: 1 residues within 4Å: Chain D: N.154 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.154 NAG.14: 2 residues within 4Å: Chain D: Q.15, N.23 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.15, D:N.23 NAG.15: 1 residues within 4Å: Chain G: N.11 No protein-ligand interaction detected (PLIP) NAG.16: 2 residues within 4Å: Chain G: Q.15, N.23 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:Q.15, G:N.23

1 x BMA: beta-D-mannopyranose(Non-covalent)

BMA.12: 3 residues within 4Å: Chain C: K.19, Y.80 Ligands: NAG-NAG-MAN-MAN.1 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.19

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: ADG
Hemagglutinin HA2: BEH
70-1F02 Fab Heavy Chain: CFI
70-1F02 Fab Light Chain: JKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
G

G
K

B
B

E
H

H
L

C
C

F
I

I
O

J
P

K
J

L
D

Hemagglutinin HA1

Hemagglutinin HA2

70-1F02 Fab Heavy Chain

70-1F02 Fab Light Chain

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