SMTL ID : 4kvn.1

Crystal structure of Fab 39.29 in complex with Influenza Hemagglutinin A/Perth/16/2009 (H3N2)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

hetero-3-3-3-mer

Ligands

6 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: 10 residues within 4Å: Chain A: T.18, T.31, N.32, A.33 Chain B: P.100, V.101, F.102, G.103, Y.110 Chain C: Y.48 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:P.100 NAG-NAG-BMA.2: 6 residues within 4Å: Chain A: N.159, T.161, L.238 Chain D: S.213, R.216 Ligands: NAG-NAG.3 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.216 NAG-NAG-BMA.11: 10 residues within 4Å: Chain D: T.18, T.31, N.32, A.33 Chain E: P.100, V.101, F.102, G.103, Y.110 Chain F: Y.48 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:Y.48 Hydrophobic interactions: E:P.100 NAG-NAG-BMA.12: 6 residues within 4Å: Chain D: N.159, T.161, L.238 Chain G: S.213, R.216 Ligands: NAG-NAG.13 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:R.216 NAG-NAG-BMA.21: 10 residues within 4Å: Chain G: T.18, T.31, N.32, A.33 Chain H: P.100, V.101, F.102, G.103, Y.110 Chain I: Y.48 2 PLIP interactions: 1 interactions with chain H, 1 interactions with chain I Hydrophobic interactions: H:P.100 Hydrogen bonds: I:Y.48 NAG-NAG-BMA.22: 6 residues within 4Å: Chain A: S.213, R.216 Chain G: N.159, T.161, L.238 Ligands: NAG-NAG.23 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.216

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.3: 8 residues within 4Å: Chain A: A.157, N.159, R.195, N.240, T.242 Chain D: D.182, I.211 Ligands: NAG-NAG-BMA.2 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:I.211 Hydrogen bonds: D:D.182 NAG-NAG.13: 8 residues within 4Å: Chain D: A.157, N.159, R.195, N.240, T.242 Chain G: D.182, I.211 Ligands: NAG-NAG-BMA.12 2 PLIP interactions: 2 interactions with chain G Hydrophobic interactions: G:I.211 Hydrogen bonds: G:D.182 NAG-NAG.23: 8 residues within 4Å: Chain A: D.182, I.211 Chain G: A.157, N.159, R.195, N.240, T.242 Ligands: NAG-NAG-BMA.22 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.211 Hydrogen bonds: A:D.182

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

NAG.4: 3 residues within 4Å: Chain A: K.56, N.57, Y.88 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.56 Hydrogen bonds: A:N.57 NAG.5: 2 residues within 4Å: Chain A: N.120, T.122 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.122 NAG.6: 2 residues within 4Å: Chain A: Q.126, N.127 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Q.126 Hydrogen bonds: A:Q.126 NAG.7: 3 residues within 4Å: Chain A: P.278, N.279, N.292 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.292 NAG.8: 3 residues within 4Å: Chain A: G.473, N.477, T.479 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.479 NAG.14: 3 residues within 4Å: Chain D: K.56, N.57, Y.88 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:K.56 Hydrogen bonds: D:N.57 NAG.15: 2 residues within 4Å: Chain D: N.120, T.122 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:T.122 NAG.16: 2 residues within 4Å: Chain D: Q.126, N.127 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:Q.126 Hydrogen bonds: D:Q.126 NAG.17: 3 residues within 4Å: Chain D: P.278, N.279, N.292 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.292 NAG.18: 3 residues within 4Å: Chain D: G.473, N.477, T.479 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:T.479 Hydrogen bonds: D:T.479 NAG.24: 3 residues within 4Å: Chain G: K.56, N.57, Y.88 2 PLIP interactions: 2 interactions with chain G Hydrophobic interactions: G:K.56 Hydrogen bonds: G:N.57 NAG.25: 2 residues within 4Å: Chain G: N.120, T.122 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:T.122 NAG.26: 2 residues within 4Å: Chain G: Q.126, N.127 2 PLIP interactions: 2 interactions with chain G Hydrophobic interactions: G:Q.126 Hydrogen bonds: G:Q.126 NAG.27: 3 residues within 4Å: Chain G: P.278, N.279, N.292 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:N.292 NAG.28: 3 residues within 4Å: Chain G: G.473, N.477, T.479 2 PLIP interactions: 2 interactions with chain G Hydrophobic interactions: G:T.479 Hydrogen bonds: G:T.479

3 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.9: 7 residues within 4Å: Chain C: V.27, H.30, S.66, G.67 Chain D: N.25, D.26, Q.27 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:D.26, D:D.26, D:D.26, D:D.26, D:Q.27, C:G.67 Salt bridges: C:H.30 PO4.19: 7 residues within 4Å: Chain F: V.27, H.30, S.66, G.67 Chain G: N.25, D.26, Q.27 7 PLIP interactions: 5 interactions with chain G, 2 interactions with chain F Hydrogen bonds: G:D.26, G:D.26, G:D.26, G:D.26, G:Q.27, F:G.67 Salt bridges: F:H.30 PO4.29: 7 residues within 4Å: Chain A: N.25, D.26, Q.27 Chain I: V.27, H.30, S.66, G.67 7 PLIP interactions: 2 interactions with chain I, 5 interactions with chain A Hydrogen bonds: I:G.67, A:D.26, A:D.26, A:D.26, A:D.26, A:Q.27 Salt bridges: I:H.30

3 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.10: 7 residues within 4Å: Chain B: G.41, K.42 Chain C: A.8, V.84, Y.86, G.101, G.102 No protein-ligand interaction detected (PLIP) PGE.20: 7 residues within 4Å: Chain E: G.41, K.42 Chain F: A.8, V.84, Y.86, G.101, G.102 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:Y.86 PGE.30: 7 residues within 4Å: Chain H: G.41, K.42 Chain I: A.8, V.84, Y.86, G.101, G.102 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nakamura, G. et al., A Novel In vivo Human Plasmablast Enrichment Technique Allows Rapid Identification of Therapeutic Anti-Influenza A Antibodies. Cell Host Microbe (2013)

Release Date

2013-08-07

Peptides

Hemagglutinin: ADG
Human IgG Heavy Chain: BEH
Human IgG Light Chain: CFI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
A

G
A

B
H

E
H

H
H

C
L

F
L

I
L

Hemagglutinin

Human IgG Heavy Chain

Human IgG Light Chain