SMTL ID : 3ztn.1

STRUCTURE OF INFLUENZA A NEUTRALIZING ANTIBODY SELECTED FROM CULTURES OF SINGLE HUMAN PLASMA CELLS IN COMPLEX WITH HUMAN H1 INFLUENZA HAEMAGGLUTININ.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

hetero-3-3-3-3-mer

Ligands

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

NAG-NAG.1: 7 residues within 4Å: Chain A: N.64, E.66, D.86, N.87, C.90, A.135, P.137 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 1 residues within 4Å: Chain A: N.23 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 7 residues within 4Å: Chain E: N.64, E.66, D.86, N.87, C.90, A.135, P.137 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 1 residues within 4Å: Chain E: N.23 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 7 residues within 4Å: Chain I: N.64, E.66, D.86, N.87, C.90, A.135, P.137 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 1 residues within 4Å: Chain I: N.23 No protein-ligand interaction detected (PLIP)

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.2: 10 residues within 4Å: Chain A: K.36, N.38, A.285, N.287 Chain C: D.54, A.55, R.72, D.73, N.74, S.75 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:A.55 Hydrogen bonds: C:N.74, C:S.75, C:D.73 NAG-NAG-BMA.13: 10 residues within 4Å: Chain E: K.36, N.38, A.285, N.287 Chain G: D.54, A.55, R.72, D.73, N.74, S.75 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:A.55 Hydrogen bonds: G:N.74, G:S.75, G:D.73 NAG-NAG-BMA.24: 10 residues within 4Å: Chain I: K.36, N.38, A.285, N.287 Chain K: D.54, A.55, R.72, D.73, N.74, S.75 1 PLIP interactions: 1 interactions with chain K Hydrophobic interactions: K:A.55 Hydrogen bonds: K:N.74, K:S.75, K:D.73

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

NAG.4: 3 residues within 4Å: Chain A: N.11 Chain B: V.18 Ligands: GOL.10 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.18 NAG.5: 3 residues within 4Å: Chain A: G.46, D.274, N.276 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.274 NAG.15: 3 residues within 4Å: Chain E: N.11 Chain F: V.18 Ligands: GOL.21 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:V.18 NAG.16: 3 residues within 4Å: Chain E: G.46, D.274, N.276 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:D.274 NAG.26: 3 residues within 4Å: Chain I: N.11 Chain J: V.18 Ligands: GOL.32 1 PLIP interactions: 1 interactions with chain J Hydrophobic interactions: J:V.18 NAG.27: 3 residues within 4Å: Chain I: G.46, D.274, N.276 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:D.274

15 x SO4: SULFATE ION(Non-functional Binders)

SO4.6: 2 residues within 4Å: Chain A: H.37, K.283 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.37 SO4.7: 2 residues within 4Å: Chain A: K.311, R.313 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.31 Salt bridges: A:K.311, A:R.313 SO4.8: 2 residues within 4Å: Chain A: N.31, R.313 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.31 Salt bridges: A:R.313 SO4.9: 4 residues within 4Å: Chain A: V.132, T.133, A.134, Q.223 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.133, A:T.133, A:A.134 SO4.11: 4 residues within 4Å: Chain B: L.38, K.39 Chain D: Q.27, R.97 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.27 Salt bridges: D:R.97 SO4.17: 2 residues within 4Å: Chain E: H.37, K.283 1 PLIP interactions: 1 interactions with chain E Salt bridges: E:H.37 SO4.18: 2 residues within 4Å: Chain E: K.311, R.313 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:N.31 Salt bridges: E:K.311, E:R.313 SO4.19: 2 residues within 4Å: Chain E: N.31, R.313 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.31 Salt bridges: E:R.313 SO4.20: 4 residues within 4Å: Chain E: V.132, T.133, A.134, Q.223 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:T.133, E:A.134 SO4.22: 4 residues within 4Å: Chain F: L.38, K.39 Chain H: Q.27, R.97 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:Q.27 Salt bridges: H:R.97 SO4.28: 2 residues within 4Å: Chain I: H.37, K.283 1 PLIP interactions: 1 interactions with chain I Salt bridges: I:H.37 SO4.29: 2 residues within 4Å: Chain I: K.311, R.313 3 PLIP interactions: 3 interactions with chain I Hydrogen bonds: I:N.31 Salt bridges: I:K.311, I:R.313 SO4.30: 2 residues within 4Å: Chain I: N.31, R.313 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:N.31 Salt bridges: I:R.313 SO4.31: 4 residues within 4Å: Chain I: V.132, T.133, A.134, Q.223 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:T.133, I:A.134 SO4.33: 4 residues within 4Å: Chain J: L.38, K.39 Chain L: Q.27, R.97 2 PLIP interactions: 2 interactions with chain L Hydrogen bonds: L:Q.27 Salt bridges: L:R.97

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 7 residues within 4Å: Chain A: H.8, N.10, N.11, H.28 Chain C: Y.57, Y.107 Ligands: NAG.4 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:H.8, A:N.10, A:N.11, C:Y.57, C:Y.57 GOL.21: 7 residues within 4Å: Chain E: H.8, N.10, N.11, H.28 Chain G: Y.57, Y.107 Ligands: NAG.15 5 PLIP interactions: 2 interactions with chain G, 3 interactions with chain E Hydrogen bonds: G:Y.57, G:Y.57, E:H.8, E:N.10, E:N.11 GOL.32: 7 residues within 4Å: Chain I: H.8, N.10, N.11, H.28 Chain K: Y.57, Y.107 Ligands: NAG.26 5 PLIP interactions: 2 interactions with chain K, 3 interactions with chain I Hydrogen bonds: K:Y.57, K:Y.57, I:H.8, I:N.10, I:N.11

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Corti, D. et al., A Neutralizing Antibody Selected from Plasma Cells that Binds to Group 1 and Group 2 Influenza a Hemagglutinins. Science (2011)

Release Date

2011-08-10

Peptides

HAEMAGGLUTININ: AEI
HAEMAGGLUTININ: BFJ
FI6V3 ANTIBODY LIGHT CHAIN: CGK
FI6V3 ANTIBODY LIGHT CHAIN: DHL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
A

I
A

B
B

F
B

J
B

C
H

G
H

K
H

D
L

H
L

L
L

HAEMAGGLUTININ

HAEMAGGLUTININ

FI6V3 ANTIBODY LIGHT CHAIN

FI6V3 ANTIBODY LIGHT CHAIN

Related Entries With Identical Sequence