SMTL ID : 6wj1.1

Crystal structure of Fab 54-4H03 bound to H1 influenza hemagglutinin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.50 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: 2 residues within 4Å: Chain A: N.14 Chain K: S.57 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: D.277, C.278, N.279 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 2 residues within 4Å: Chain F: N.154, T.156 No protein-ligand interaction detected (PLIP)

1 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.2: 6 residues within 4Å: Chain A: N.67, E.69, D.89, N.90, C.93, R.224 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: 8 residues within 4Å: Chain B: N.67, E.69, D.89, N.90, C.93, A.138, P.140, R.224 No protein-ligand interaction detected (PLIP)

1 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.5: 2 residues within 4Å: Chain B: K.25, N.26 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:K.25

1 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.6: 7 residues within 4Å: Chain C: N.67, E.69, D.89, N.90, C.93, P.140, R.224 No protein-ligand interaction detected (PLIP)

1 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.7: 3 residues within 4Å: Chain C: G.49, D.277, N.279 No protein-ligand interaction detected (PLIP)

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

NAG.9: 1 residues within 4Å: Chain A: N.290 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.290 NAG.10: 1 residues within 4Å: Chain A: N.26 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.26 NAG.11: 1 residues within 4Å: Chain B: N.14 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.14 NAG.12: 2 residues within 4Å: Chain B: D.277, N.279 No protein-ligand interaction detected (PLIP) NAG.13: 1 residues within 4Å: Chain B: N.290 No protein-ligand interaction detected (PLIP) NAG.14: 1 residues within 4Å: Chain C: N.14 No protein-ligand interaction detected (PLIP) NAG.15: 1 residues within 4Å: Chain C: N.290 No protein-ligand interaction detected (PLIP) NAG.16: 1 residues within 4Å: Chain C: N.26 No protein-ligand interaction detected (PLIP) NAG.17: 2 residues within 4Å: Chain D: N.154, T.156 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:T.156, D:T.156 NAG.18: 2 residues within 4Å: Chain E: N.154, T.156 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wu, N.C. et al., Convergent Evolution in Breadth of Two VH6-1-Encoded Influenza Antibody Clonotypes from a Single Donor. Cell Host Microbe (2020)

Release Date

2020-07-01

Peptides

Hemagglutinin HA1 chain: ABC
Hemagglutinin HA2 chain: DEF
Fab 54-4H03 heavy chain: GIK
Fab 54-4H03 light chain: HJL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
E

D
B

E
D

F
F

G
H

I
J

K
G

H
L

J
K

L
I

Hemagglutinin HA1 chain

Hemagglutinin HA2 chain

Fab 54-4H03 heavy chain

Fab 54-4H03 light chain

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