SMTL ID : 4o58.1

Crystal structure of broadly neutralizing antibody F045-092 in complex with A/Victoria/3/1975 (H3N2) influenza hemagglutinin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.75 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(Post Translational Modification)

NAG-NAG.1: 3 residues within 4Å: Chain A: N.32, T.312 Chain B: L.52 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 5 residues within 4Å: Chain A: S.39, N.279, V.291, N.292 Chain B: E.69 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 3 residues within 4Å: Chain E: N.32, T.312 Chain F: L.52 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 5 residues within 4Å: Chain E: S.39, N.279, V.291, N.292 Chain F: E.69 No protein-ligand interaction detected (PLIP) NAG-NAG.45: 3 residues within 4Å: Chain I: N.32, T.312 Chain J: L.52 No protein-ligand interaction detected (PLIP) NAG-NAG.47: 5 residues within 4Å: Chain I: S.39, N.279, V.291, N.292 Chain J: E.69 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: 5 residues within 4Å: Chain A: N.159, T.161 Chain E: S.213, P.215, W.216 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain E Hydrophobic interactions: A:T.161 Hydrogen bonds: E:W.216 NAG-NAG-BMA-MAN-MAN.24: 5 residues within 4Å: Chain E: N.159, T.161 Chain I: S.213, P.215, W.216 2 PLIP interactions: 1 interactions with chain I, 1 interactions with chain E Hydrogen bonds: I:W.216 Hydrophobic interactions: E:T.161 NAG-NAG-BMA-MAN-MAN.46: 5 residues within 4Å: Chain A: S.213, P.215, W.216 Chain I: N.159, T.161 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain I Hydrogen bonds: A:W.216 Hydrophobic interactions: I:T.161

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

NAG.4: 3 residues within 4Å: Chain A: I.56, N.57, F.88 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.56 Hydrogen bonds: A:N.57 NAG.11: 4 residues within 4Å: Chain B: A.147, G.150, S.151, N.154 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.154, B:N.154 NAG.26: 3 residues within 4Å: Chain E: I.56, N.57, F.88 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:I.56 Hydrogen bonds: E:N.57 NAG.33: 4 residues within 4Å: Chain F: A.147, G.150, S.151, N.154 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:N.154, F:N.154 NAG.48: 3 residues within 4Å: Chain I: I.56, N.57, F.88 2 PLIP interactions: 2 interactions with chain I Hydrophobic interactions: I:I.56 Hydrogen bonds: I:N.57 NAG.55: 4 residues within 4Å: Chain J: A.147, G.150, S.151, N.154 2 PLIP interactions: 2 interactions with chain J Hydrogen bonds: J:N.154, J:N.154

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

SO4.5: 4 residues within 4Å: Chain A: R.84, K.86, D.265, P.267 Ligand excluded by PLIP SO4.6: 4 residues within 4Å: Chain A: K.44, I.268, G.269, T.270 Ligand excluded by PLIP SO4.7: 1 residues within 4Å: Chain A: R.51 Ligand excluded by PLIP SO4.8: 4 residues within 4Å: Chain A: N.75, F.114, N.116, R.144 Ligand excluded by PLIP SO4.9: 3 residues within 4Å: Chain A: I.28, R.315 Chain B: A.7 Ligand excluded by PLIP SO4.12: 5 residues within 4Å: Chain B: R.127, H.159, D.160 Chain F: M.133, K.139 Ligand excluded by PLIP SO4.13: 5 residues within 4Å: Chain B: G.13, W.14, E.15, G.16, R.25 Ligand excluded by PLIP SO4.14: 2 residues within 4Å: Chain B: R.25, Q.34 Ligand excluded by PLIP SO4.15: 8 residues within 4Å: Chain C: T.33, N.35, Y.50, S.51 Chain D: Y.115, Y.116, G.117 Ligands: PEG.18 Ligand excluded by PLIP SO4.16: 2 residues within 4Å: Chain C: S.25, R.26 Ligand excluded by PLIP SO4.19: 3 residues within 4Å: Chain D: F.54, T.56, C.109 Ligand excluded by PLIP SO4.20: 7 residues within 4Å: Chain D: Y.31, E.102, Y.105, C.106, D.113, Y.114, Y.116 Ligand excluded by PLIP SO4.21: 2 residues within 4Å: Chain D: A.110, A.111 Ligand excluded by PLIP SO4.22: 2 residues within 4Å: Chain D: S.7, G.8 Ligand excluded by PLIP SO4.27: 4 residues within 4Å: Chain E: R.84, K.86, D.265, P.267 Ligand excluded by PLIP SO4.28: 4 residues within 4Å: Chain E: K.44, I.268, G.269, T.270 Ligand excluded by PLIP SO4.29: 1 residues within 4Å: Chain E: R.51 Ligand excluded by PLIP SO4.30: 4 residues within 4Å: Chain E: N.75, F.114, N.116, R.144 Ligand excluded by PLIP SO4.31: 3 residues within 4Å: Chain E: I.28, R.315 Chain F: A.7 Ligand excluded by PLIP SO4.34: 5 residues within 4Å: Chain F: R.127, H.159, D.160 Chain J: M.133, K.139 Ligand excluded by PLIP SO4.35: 5 residues within 4Å: Chain F: G.13, W.14, E.15, G.16, R.25 Ligand excluded by PLIP SO4.36: 2 residues within 4Å: Chain F: R.25, Q.34 Ligand excluded by PLIP SO4.37: 8 residues within 4Å: Chain G: T.33, N.35, Y.50, S.51 Chain H: Y.115, Y.116, G.117 Ligands: PEG.40 Ligand excluded by PLIP SO4.38: 2 residues within 4Å: Chain G: S.25, R.26 Ligand excluded by PLIP SO4.41: 3 residues within 4Å: Chain H: F.54, T.56, C.109 Ligand excluded by PLIP SO4.42: 7 residues within 4Å: Chain H: Y.31, E.102, Y.105, C.106, D.113, Y.114, Y.116 Ligand excluded by PLIP SO4.43: 2 residues within 4Å: Chain H: A.110, A.111 Ligand excluded by PLIP SO4.44: 2 residues within 4Å: Chain H: S.7, G.8 Ligand excluded by PLIP SO4.49: 4 residues within 4Å: Chain I: R.84, K.86, D.265, P.267 Ligand excluded by PLIP SO4.50: 4 residues within 4Å: Chain I: K.44, I.268, G.269, T.270 Ligand excluded by PLIP SO4.51: 1 residues within 4Å: Chain I: R.51 Ligand excluded by PLIP SO4.52: 4 residues within 4Å: Chain I: N.75, F.114, N.116, R.144 Ligand excluded by PLIP SO4.53: 3 residues within 4Å: Chain I: I.28, R.315 Chain J: A.7 Ligand excluded by PLIP SO4.56: 5 residues within 4Å: Chain B: M.133, K.139 Chain J: R.127, H.159, D.160 Ligand excluded by PLIP SO4.57: 5 residues within 4Å: Chain J: G.13, W.14, E.15, G.16, R.25 Ligand excluded by PLIP SO4.58: 2 residues within 4Å: Chain J: R.25, Q.34 Ligand excluded by PLIP SO4.59: 8 residues within 4Å: Chain K: T.33, N.35, Y.50, S.51 Chain L: Y.115, Y.116, G.117 Ligands: PEG.62 Ligand excluded by PLIP SO4.60: 2 residues within 4Å: Chain K: S.25, R.26 Ligand excluded by PLIP SO4.63: 3 residues within 4Å: Chain L: F.54, T.56, C.109 Ligand excluded by PLIP SO4.64: 7 residues within 4Å: Chain L: Y.31, E.102, Y.105, C.106, D.113, Y.114, Y.116 Ligand excluded by PLIP SO4.65: 2 residues within 4Å: Chain L: A.110, A.111 Ligand excluded by PLIP SO4.66: 2 residues within 4Å: Chain L: S.7, G.8 Ligand excluded by PLIP

9 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.10: 4 residues within 4Å: Chain A: K.301 Chain B: R.54 Chain F: Y.94, E.97 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.301, A:K.301, B:R.54 PEG.17: 7 residues within 4Å: Chain C: P.8, D.86, G.103, G.104 Chain D: Q.38, G.41, Q.42 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:P.8 Water bridges: D:G.41 PEG.18: 9 residues within 4Å: Chain C: T.33, N.35, Y.37, A.90, W.92, V.99 Chain D: Y.115, Y.116 Ligands: SO4.15 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Y.37, C:W.92 PEG.32: 4 residues within 4Å: Chain E: K.301 Chain F: R.54 Chain J: Y.94, E.97 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:K.301, E:K.301, F:R.54 PEG.39: 7 residues within 4Å: Chain G: P.8, D.86, G.103, G.104 Chain H: Q.38, G.41, Q.42 2 PLIP interactions: 1 interactions with chain H, 1 interactions with chain G Water bridges: H:G.41 Hydrogen bonds: G:P.8 PEG.40: 9 residues within 4Å: Chain G: T.33, N.35, Y.37, A.90, W.92, V.99 Chain H: Y.115, Y.116 Ligands: SO4.37 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:Y.37, G:W.92 PEG.54: 4 residues within 4Å: Chain B: Y.94, E.97 Chain I: K.301 Chain J: R.54 3 PLIP interactions: 1 interactions with chain J, 2 interactions with chain I Hydrogen bonds: J:R.54, I:K.301, I:K.301 PEG.61: 7 residues within 4Å: Chain K: P.8, D.86, G.103, G.104 Chain L: Q.38, G.41, Q.42 2 PLIP interactions: 1 interactions with chain L, 1 interactions with chain K Water bridges: L:G.41 Hydrogen bonds: K:P.8 PEG.62: 9 residues within 4Å: Chain K: T.33, N.35, Y.37, A.90, W.92, V.99 Chain L: Y.115, Y.116 Ligands: SO4.59 2 PLIP interactions: 2 interactions with chain K Hydrogen bonds: K:Y.37, K:W.92

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lee, P.S. et al., Receptor mimicry by antibody F045-092 facilitates universal binding to the H3 subtype of influenza virus. Nat Commun (2014)

Release Date

2014-04-16

Peptides

Hemagglutinin HA1 chain: AEI
Hemagglutinin HA2 chain: BFJ
Fab F045-092 light chain: CGK
Fab F045-092 heavy chain: DHL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
A

I
A

B
B

F
B

J
B

C
L

G
L

K
L

D
H

H
H

L
H

Hemagglutinin HA1 chain

Hemagglutinin HA2 chain

Fab F045-092 light chain

Fab F045-092 heavy chain

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