SMTL ID : 4mhh.1 (4 other biounits)

Crystal structure of Fab H5M9 in complex with influenza virus hemagglutinin from A/Viet Nam/1203/2004 (H5N1)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.56 Å

Oligo State

hetero-3-3-3-3-mer

Ligands

3 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.1: 5 residues within 4Å: Chain A: N.169, N.240, D.241, A.242 Chain B: S.221 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN-MAN-MAN.7: 4 residues within 4Å: Chain B: N.169, N.240, A.242 Chain C: S.221 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN-MAN-MAN.12: 4 residues within 4Å: Chain A: S.221 Chain C: N.169, N.240, A.242 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.2: 2 residues within 4Å: Chain A: N.279, N.290 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 1 residues within 4Å: Chain A: N.158 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain A: N.14, N.15 Chain G: Q.15 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 1 residues within 4Å: Chain B: N.27 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 2 residues within 4Å: Chain B: N.279, N.290 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 1 residues within 4Å: Chain B: N.158 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 1 residues within 4Å: Chain B: N.15 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 2 residues within 4Å: Chain C: Q.19, N.27 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 2 residues within 4Å: Chain C: N.279, N.290 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 2 residues within 4Å: Chain C: N.15 Chain I: Q.15 No protein-ligand interaction detected (PLIP)

3 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(Post Translational Modification)

NAG-NAG-MAN.5: 2 residues within 4Å: Chain A: Q.19, N.27 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.14: 1 residues within 4Å: Chain C: N.158 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.16: 6 residues within 4Å: Chain G: E.147, C.148, E.150, S.151, N.154, T.156 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:E.147

1 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(Post Translational Modification)

NAG-NAG-MAN-MAN.17: 6 residues within 4Å: Chain H: E.147, E.150, S.151, N.154, T.156, Y.162 No protein-ligand interaction detected (PLIP)

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

NAG.18: 1 residues within 4Å: Chain D: N.67 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.67 NAG.19: 1 residues within 4Å: Chain E: N.67 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.67 NAG.20: 2 residues within 4Å: Chain F: R.58, N.67 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:N.67 NAG.21: 2 residues within 4Å: Chain I: N.154, T.156 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:N.154, I:T.156

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhu, X. et al., A Unique and Conserved Neutralization Epitope in H5N1 Influenza Viruses Identified by an Antibody against the A/Goose/Guangdong/1/96 Hemagglutinin. J.Virol. (2013)

Release Date

2013-10-02

Peptides

Hemagglutinin HA1 chain: ABC
H5M9 antibody, light chain (kappa): DEF
Hemagglutinin HA2 chain: GHI
H5M9 antibody, heavy chain (IgG1): JKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
E

D
L

E
I

F
K

G
B

H
D

I
F

J
H

K
G

L
J

Hemagglutinin HA1 chain

H5M9 antibody, light chain (kappa)

Hemagglutinin HA2 chain

H5M9 antibody, heavy chain (IgG1)

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