SMTL ID : 4gms.1

Crystal structure of heterosubtypic Fab S139/1 in complex with influenza A H3 hemagglutinin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.95 Å

Oligo State

hetero-3-3-3-3-mer

Ligands

5 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: 3 residues within 4Å: Chain A: I.53, N.54, F.85 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 5 residues within 4Å: Chain A: S.36, N.276, V.288, N.289 Chain B: E.69 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain C: I.53, N.54, F.85 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 2 residues within 4Å: Chain E: N.117, T.119 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain H: N.73, S.75, S.76 Ligands: NAG-NAG-BMA-MAN-MAN.10 No protein-ligand interaction detected (PLIP)

3 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: 8 residues within 4Å: Chain A: N.156, T.158, I.233 Chain C: S.210, R.211, P.212, W.213 Chain J: S.75 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:W.213 Hydrophobic interactions: A:I.233 NAG-NAG-BMA-MAN-MAN.5: 7 residues within 4Å: Chain C: N.156, T.158, I.233 Chain E: S.210, R.211, P.212, W.213 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain C Hydrogen bonds: E:W.213 Hydrophobic interactions: C:I.233 NAG-NAG-BMA-MAN-MAN.10: 7 residues within 4Å: Chain A: S.210, P.212, W.213 Chain E: N.156, T.158, I.233 Ligands: NAG-NAG.12 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain A Hydrophobic interactions: E:I.233 Hydrogen bonds: A:W.213

2 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.6: 5 residues within 4Å: Chain C: S.36, N.276, V.288, N.289 Chain D: E.69 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.8: 3 residues within 4Å: Chain E: I.53, N.54, F.85 No protein-ligand interaction detected (PLIP)

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.7: 4 residues within 4Å: Chain E: N.29, T.31, T.309 Chain F: L.52 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.11: 5 residues within 4Å: Chain E: S.36, N.276, V.288, N.289 Chain F: E.69 No protein-ligand interaction detected (PLIP)

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

NAG.13: 3 residues within 4Å: Chain A: N.29, T.309 Chain B: L.52 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.29 NAG.14: 2 residues within 4Å: Chain A: N.117, T.119 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.117 NAG.20: 2 residues within 4Å: Chain B: N.154, T.156 No protein-ligand interaction detected (PLIP) NAG.25: 3 residues within 4Å: Chain C: N.29, T.309 Chain D: L.52 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.29 NAG.26: 2 residues within 4Å: Chain C: N.117, T.119 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.117 NAG.30: 2 residues within 4Å: Chain D: N.154, T.156 No protein-ligand interaction detected (PLIP) NAG.36: 2 residues within 4Å: Chain F: N.154, T.156 No protein-ligand interaction detected (PLIP) NAG.39: 3 residues within 4Å: Chain J: N.73, S.75, S.76 2 PLIP interactions: 2 interactions with chain J Hydrogen bonds: J:N.73, J:S.76 NAG.41: 3 residues within 4Å: Chain L: N.73, S.75, S.76 1 PLIP interactions: 1 interactions with chain L Hydrogen bonds: L:N.73

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

SO4.15: 2 residues within 4Å: Chain A: R.48, D.76 Ligand excluded by PLIP SO4.16: 5 residues within 4Å: Chain A: D.135, S.136 Chain H: T.58, Y.60, F.70 Ligand excluded by PLIP SO4.17: 4 residues within 4Å: Chain A: V.93, P.94, D.95, Y.96 Ligand excluded by PLIP SO4.18: 4 residues within 4Å: Chain A: E.80, Y.96, R.100, R.260 Ligand excluded by PLIP SO4.19: 3 residues within 4Å: Chain A: K.41, G.266, T.267 Ligand excluded by PLIP SO4.21: 4 residues within 4Å: Chain B: R.127, H.159, D.160 Chain D: K.139 Ligand excluded by PLIP SO4.22: 4 residues within 4Å: Chain B: K.139 Chain F: R.127, H.159, D.160 Ligand excluded by PLIP SO4.23: 5 residues within 4Å: Chain A: E.316 Chain B: W.14, E.15, G.16, R.25 Ligand excluded by PLIP SO4.27: 2 residues within 4Å: Chain C: R.48, K.74 Ligand excluded by PLIP SO4.28: 5 residues within 4Å: Chain C: D.135, S.136 Chain J: T.58, Y.60, T.69 Ligand excluded by PLIP SO4.29: 4 residues within 4Å: Chain C: N.72, F.111, N.113, R.141 Ligand excluded by PLIP SO4.31: 4 residues within 4Å: Chain D: R.127, H.159, D.160 Chain F: K.139 Ligand excluded by PLIP SO4.32: 5 residues within 4Å: Chain D: G.13, W.14, E.15, G.16, R.25 Ligand excluded by PLIP SO4.34: 5 residues within 4Å: Chain E: D.135, S.136 Chain L: T.58, Y.60, F.70 Ligand excluded by PLIP SO4.37: 5 residues within 4Å: Chain F: G.13, W.14, E.15, G.16, R.25 Ligand excluded by PLIP SO4.38: 3 residues within 4Å: Chain H: Y.27, T.28, Y.32 Ligand excluded by PLIP SO4.40: 3 residues within 4Å: Chain J: Y.27, T.28, Y.32 Ligand excluded by PLIP SO4.42: 3 residues within 4Å: Chain L: Y.27, T.28, Y.32 Ligand excluded by PLIP

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.24: 5 residues within 4Å: Chain A: K.298 Chain B: R.54, V.55, L.99 Chain D: Y.94 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.54, B:R.54, B:V.55, A:K.298, A:K.298 GOL.33: 4 residues within 4Å: Chain C: K.298 Chain D: R.54, L.99 Chain F: Y.94 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:R.54, D:R.54, C:K.298, C:K.298

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.35: 4 residues within 4Å: Chain C: R.199 Chain E: S.86, Y.91, R.215 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:R.215, E:R.215

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lee, P.S. et al., Heterosubtypic antibody recognition of the influenza virus hemagglutinin receptor binding site enhanced by avidity. Proc.Natl.Acad.Sci.USA (2012)

Release Date

2012-10-03

Peptides

Hemagglutinin HA1 chain: ACE
Hemagglutinin HA2 chain: BDF
Fab S139/1 light chain: GIK
Fab S139/1 heavy chain: HJL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

B
B

D
D

F
F

G
L

I
M

K
N

H
H

J
I

L
J

Hemagglutinin HA1 chain

Hemagglutinin HA2 chain

Fab S139/1 light chain

Fab S139/1 heavy chain

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