SMTL ID : 8t1g.1

The crystal structure of hemagglutinin form a h7n9 influenza virus (a/shanghai/1/2013) in complex with antibody 1E11

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.50 Å

Oligo State

hetero-3-3-3-3-mer

Ligands

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.1: 5 residues within 4Å: Chain A: V.27, N.28 Chain J: R.99, D.101 Chain K: D.33 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:R.99, J:D.101 NAG-NAG-BMA.3: 6 residues within 4Å: Chain C: V.10, V.27, N.28 Chain G: R.99, D.101 Chain I: D.33 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:R.99, G:R.99, G:S.103 NAG-NAG-BMA.5: 6 residues within 4Å: Chain E: V.27, N.28 Chain H: R.99, D.101, S.103 Chain L: D.33 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:R.99, H:R.99, H:S.103

2 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: R.81, R.291 Chain B: E.69, K.75, N.79, N.82 Chain C: E.104 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.291, A:R.81 NAG-NAG-BMA-MAN.6: 7 residues within 4Å: Chain A: E.104 Chain E: R.81, R.291 Chain F: E.69, K.75, N.79, N.82 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN: 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.4: 6 residues within 4Å: Chain C: R.291 Chain D: E.69, E.72, K.75, N.79, N.82 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:E.69

3 x CA: CALCIUM ION(Non-functional Binders)(Non-covalent)

CA.7: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.10: 2 residues within 4Å: Chain C: D.109, K.110 No protein-ligand interaction detected (PLIP) CA.13: 1 residues within 4Å: Chain E: D.109 No protein-ligand interaction detected (PLIP)

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

NAG.8: 2 residues within 4Å: Chain A: K.164, N.231 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.231 NAG.9: 4 residues within 4Å: Chain B: D.147, A.150, N.154, T.156 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.154 NAG.11: 2 residues within 4Å: Chain C: K.160, N.231 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.160, C:N.231 NAG.12: 4 residues within 4Å: Chain D: D.147, A.150, N.154, T.156 No protein-ligand interaction detected (PLIP) NAG.14: 4 residues within 4Å: Chain E: N.161, T.162, K.164, N.231 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:K.164, E:N.231 NAG.15: 4 residues within 4Å: Chain F: D.147, A.150, N.154, T.156 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:D.147, F:N.154

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mantus, G.E. et al., Distinct binding modes drive the broad neutralization profile of two persistent influenza hemagglutinin stem-specific antibody lineages. Structure (2025)

Release Date

2024-05-29

Peptides

Hemagglutinin HA1: ACE
Hemagglutinin HA2: BDF
1E11 Fab Heavy chain: GHJ
1E11 Fab Light chain: IKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

B
B

D
D

F
F

G
G

H
H

J
J

I
I

K
K

L
L

Hemagglutinin HA1

Hemagglutinin HA2

1E11 Fab Heavy chain

1E11 Fab Light chain

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