SMTL ID : 3sdy.1

Crystal Structure of Broadly Neutralizing Antibody CR8020 Bound to the Influenza A H3 Hemagglutinin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.85 Å

Oligo State

hetero-3-3-3-3-mer

Ligands

3 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.1: 7 residues within 4Å: Chain A: H.12, N.32, A.33, T.34, T.312 Chain B: W.21, N.49 0 PLIP interactions: NAG-NAG-BMA-MAN.16: 7 residues within 4Å: Chain E: H.12, N.32, A.33, T.34, T.312 Chain F: W.21, N.49 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.31: 7 residues within 4Å: Chain I: H.12, N.32, A.33, T.34, T.312 Chain J: W.21, N.49 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN- FUC: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-FUC.2: 6 residues within 4Å: Chain A: Q.74, N.75, E.113, F.114, I.115, R.144 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:N.75 NAG-NAG-BMA-MAN-MAN-FUC.17: 6 residues within 4Å: Chain E: Q.74, N.75, E.113, F.114, I.115, R.144 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:N.75 NAG-NAG-BMA-MAN-MAN-FUC.32: 6 residues within 4Å: Chain I: Q.74, N.75, E.113, F.114, I.115, R.144 1 PLIP interactions: 1 interactions with chain I Hydrophobic interactions: I:N.75

3 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.3: 9 residues within 4Å: Chain A: V.157, N.159, T.161, V.236, V.238, N.240 Chain I: S.213, P.215, W.216 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain I Hydrophobic interactions: A:V.236, A:V.238, I:P.215 Hydrogen bonds: I:W.216 NAG-NAG-BMA-MAN.18: 9 residues within 4Å: Chain A: S.213, P.215, W.216 Chain E: V.157, N.159, T.161, V.236, V.238, N.240 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain A Hydrophobic interactions: E:V.236, E:V.238, A:P.215 Hydrogen bonds: A:W.216 NAG-NAG-BMA-MAN.33: 9 residues within 4Å: Chain E: S.213, P.215, W.216 Chain I: V.157, N.159, T.161, V.236, V.238, N.240 4 PLIP interactions: 2 interactions with chain I, 2 interactions with chain E Hydrophobic interactions: I:V.236, I:V.238, E:P.215 Hydrogen bonds: E:W.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.4: 8 residues within 4Å: Chain A: S.39, S.40, P.278, N.279, V.291, N.292, K.293 Chain B: E.69 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 8 residues within 4Å: Chain E: S.39, S.40, P.278, N.279, V.291, N.292, K.293 Chain F: E.69 No protein-ligand interaction detected (PLIP) NAG-NAG.34: 8 residues within 4Å: Chain I: S.39, S.40, P.278, N.279, V.291, N.292, K.293 Chain J: E.69 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- FUC: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-FUC.5: 8 residues within 4Å: Chain B: N.146, A.147, E.150, S.151, N.154, T.156 Chain D: S.31, M.32 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:M.32 NAG-NAG-BMA-FUC.20: 8 residues within 4Å: Chain F: N.146, A.147, E.150, S.151, N.154, T.156 Chain H: S.31, M.32 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:M.32 NAG-NAG-BMA-FUC.35: 8 residues within 4Å: Chain J: N.146, A.147, E.150, S.151, N.154, T.156 Chain L: S.31, M.32 1 PLIP interactions: 1 interactions with chain L Hydrogen bonds: L:M.32

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

SO4.6: 4 residues within 4Å: Chain A: I.28, R.315 Chain B: G.1, A.7 Ligand excluded by PLIP SO4.7: 5 residues within 4Å: Chain A: A.298 Chain B: K.58, T.59, N.60, K.62 Ligand excluded by PLIP SO4.8: 5 residues within 4Å: Chain B: R.127, H.159, D.160 Chain J: M.133, K.139 Ligand excluded by PLIP SO4.9: 3 residues within 4Å: Chain B: K.39, K.121, G.155 Ligand excluded by PLIP SO4.10: 3 residues within 4Å: Chain D: S.54, R.55, R.56 Ligand excluded by PLIP SO4.11: 4 residues within 4Å: Chain D: P.61, D.62, R.63, R.79 Ligand excluded by PLIP SO4.12: 3 residues within 4Å: Chain D: S.54, R.56, S.65 Ligand excluded by PLIP SO4.13: 3 residues within 4Å: Chain D: P.61, R.63, A.83 Ligand excluded by PLIP SO4.14: 2 residues within 4Å: Chain D: K.192, R.213 Ligand excluded by PLIP SO4.15: 3 residues within 4Å: Chain D: K.41, Q.44, R.47 Ligand excluded by PLIP SO4.21: 4 residues within 4Å: Chain E: I.28, R.315 Chain F: G.1, A.7 Ligand excluded by PLIP SO4.22: 5 residues within 4Å: Chain E: A.298 Chain F: K.58, T.59, N.60, K.62 Ligand excluded by PLIP SO4.23: 5 residues within 4Å: Chain B: M.133, K.139 Chain F: R.127, H.159, D.160 Ligand excluded by PLIP SO4.24: 3 residues within 4Å: Chain F: K.39, K.121, G.155 Ligand excluded by PLIP SO4.25: 3 residues within 4Å: Chain H: S.54, R.55, R.56 Ligand excluded by PLIP SO4.26: 4 residues within 4Å: Chain H: P.61, D.62, R.63, R.79 Ligand excluded by PLIP SO4.27: 3 residues within 4Å: Chain H: S.54, R.56, S.65 Ligand excluded by PLIP SO4.28: 3 residues within 4Å: Chain H: P.61, R.63, A.83 Ligand excluded by PLIP SO4.29: 2 residues within 4Å: Chain H: K.192, R.213 Ligand excluded by PLIP SO4.30: 3 residues within 4Å: Chain H: K.41, Q.44, R.47 Ligand excluded by PLIP SO4.36: 4 residues within 4Å: Chain I: I.28, R.315 Chain J: G.1, A.7 Ligand excluded by PLIP SO4.37: 5 residues within 4Å: Chain I: A.298 Chain J: K.58, T.59, N.60, K.62 Ligand excluded by PLIP SO4.38: 5 residues within 4Å: Chain F: M.133, K.139 Chain J: R.127, H.159, D.160 Ligand excluded by PLIP SO4.39: 3 residues within 4Å: Chain J: K.39, K.121, G.155 Ligand excluded by PLIP SO4.40: 3 residues within 4Å: Chain L: S.54, R.55, R.56 Ligand excluded by PLIP SO4.41: 4 residues within 4Å: Chain L: P.61, D.62, R.63, R.79 Ligand excluded by PLIP SO4.42: 3 residues within 4Å: Chain L: S.54, R.56, S.65 Ligand excluded by PLIP SO4.43: 3 residues within 4Å: Chain L: P.61, R.63, A.83 Ligand excluded by PLIP SO4.44: 2 residues within 4Å: Chain L: K.192, R.213 Ligand excluded by PLIP SO4.45: 3 residues within 4Å: Chain L: K.41, Q.44, R.47 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ekiert, D.C. et al., A highly conserved neutralizing epitope on group 2 influenza A viruses. Science (2011)

Release Date

2011-07-20

Peptides

Hemagglutinin HA1 chain: AEI
Hemagglutinin HA2 chain: BFJ
Antibody CR8020, Heavy Chain: CGK
Antibody CR8020, 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

Hemagglutinin HA1 chain

Hemagglutinin HA2 chain

Antibody CR8020, Heavy Chain

Antibody CR8020, Light Chain

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