SMTL ID : 4fqi.1

Crystal Structure of Fab CR9114 in Complex with a H5N1 influenza virus hemagglutinin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.71 Å

Oligo State

hetero-3-3-3-3-mer

Ligands

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.1: 5 residues within 4Å: Chain A: N.169, N.240, D.241, A.242 Chain I: S.221 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.240 NAG-NAG.17: 5 residues within 4Å: Chain A: S.221 Chain E: N.169, N.240, D.241, A.242 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.240 NAG-NAG.33: 5 residues within 4Å: Chain E: S.221 Chain I: N.169, N.240, D.241, A.242 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:N.240

33 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 7 residues within 4Å: Chain A: V.20, D.21, R.314, L.315, V.316 Chain B: V.100, N.104 Ligand excluded by PLIP EDO.3: 6 residues within 4Å: Chain A: A.62, D.92, L.93, D.98, F.99, Y.102 Ligand excluded by PLIP EDO.4: 8 residues within 4Å: Chain A: G.97, D.98, H.184, R.216, R.229, E.231 Chain E: T.208, N.210 Ligand excluded by PLIP EDO.5: 8 residues within 4Å: Chain A: W.64, F.74, I.75, N.76, V.77, F.115, K.117, Y.258 Ligand excluded by PLIP EDO.7: 1 residues within 4Å: Chain A: Q.119 Ligand excluded by PLIP EDO.10: 4 residues within 4Å: Chain B: W.14, H.25, Y.34 Ligands: GOL.9 Ligand excluded by PLIP EDO.11: 1 residues within 4Å: Ligands: EDO.12 Ligand excluded by PLIP EDO.12: 7 residues within 4Å: Chain B: Q.42, D.46 Chain C: N.31, Y.32, G.100, N.101 Ligands: EDO.11 Ligand excluded by PLIP EDO.13: 5 residues within 4Å: Chain B: D.46, T.49, N.50 Chain C: T.28, N.31 Ligand excluded by PLIP EDO.14: 5 residues within 4Å: Chain B: A.36, D.37, K.38, E.39, R.153 Ligand excluded by PLIP EDO.16: 7 residues within 4Å: Chain B: D.19, A.36, K.38 Chain C: N.101, Y.102, Y.103, Y.105 Ligand excluded by PLIP EDO.18: 7 residues within 4Å: Chain E: V.20, D.21, R.314, L.315, V.316 Chain F: V.100, N.104 Ligand excluded by PLIP EDO.19: 6 residues within 4Å: Chain E: A.62, D.92, L.93, D.98, F.99, Y.102 Ligand excluded by PLIP EDO.20: 8 residues within 4Å: Chain E: G.97, D.98, H.184, R.216, R.229, E.231 Chain I: T.208, N.210 Ligand excluded by PLIP EDO.21: 8 residues within 4Å: Chain E: W.64, F.74, I.75, N.76, V.77, F.115, K.117, Y.258 Ligand excluded by PLIP EDO.23: 1 residues within 4Å: Chain E: Q.119 Ligand excluded by PLIP EDO.26: 4 residues within 4Å: Chain F: W.14, H.25, Y.34 Ligands: GOL.25 Ligand excluded by PLIP EDO.27: 1 residues within 4Å: Ligands: EDO.28 Ligand excluded by PLIP EDO.28: 7 residues within 4Å: Chain F: Q.42, D.46 Chain G: N.31, Y.32, G.100, N.101 Ligands: EDO.27 Ligand excluded by PLIP EDO.29: 5 residues within 4Å: Chain F: D.46, T.49, N.50 Chain G: T.28, N.31 Ligand excluded by PLIP EDO.30: 5 residues within 4Å: Chain F: A.36, D.37, K.38, E.39, R.153 Ligand excluded by PLIP EDO.32: 7 residues within 4Å: Chain F: D.19, A.36, K.38 Chain G: N.101, Y.102, Y.103, Y.105 Ligand excluded by PLIP EDO.34: 7 residues within 4Å: Chain I: V.20, D.21, R.314, L.315, V.316 Chain J: V.100, N.104 Ligand excluded by PLIP EDO.35: 6 residues within 4Å: Chain I: A.62, D.92, L.93, D.98, F.99, Y.102 Ligand excluded by PLIP EDO.36: 8 residues within 4Å: Chain A: T.208, N.210 Chain I: G.97, D.98, H.184, R.216, R.229, E.231 Ligand excluded by PLIP EDO.37: 8 residues within 4Å: Chain I: W.64, F.74, I.75, N.76, V.77, F.115, K.117, Y.258 Ligand excluded by PLIP EDO.39: 1 residues within 4Å: Chain I: Q.119 Ligand excluded by PLIP EDO.42: 4 residues within 4Å: Chain J: W.14, H.25, Y.34 Ligands: GOL.41 Ligand excluded by PLIP EDO.43: 1 residues within 4Å: Ligands: EDO.44 Ligand excluded by PLIP EDO.44: 7 residues within 4Å: Chain J: Q.42, D.46 Chain K: N.31, Y.32, G.100, N.101 Ligands: EDO.43 Ligand excluded by PLIP EDO.45: 5 residues within 4Å: Chain J: D.46, T.49, N.50 Chain K: T.28, N.31 Ligand excluded by PLIP EDO.46: 5 residues within 4Å: Chain J: A.36, D.37, K.38, E.39, R.153 Ligand excluded by PLIP EDO.48: 7 residues within 4Å: Chain J: D.19, A.36, K.38 Chain K: N.101, Y.102, Y.103, Y.105 Ligand excluded by PLIP

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

NAG.6: 2 residues within 4Å: Chain A: N.15 Chain B: Q.15 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.15, B:Q.15 Water bridges: B:Q.15 NAG.8: 1 residues within 4Å: Chain A: N.27 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.27 NAG.15: 5 residues within 4Å: Chain B: E.147, E.150, S.151, N.154, T.156 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.147, B:T.156 Water bridges: B:N.154 NAG.22: 2 residues within 4Å: Chain E: N.15 Chain F: Q.15 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:Q.15, E:N.15 Water bridges: F:Q.15 NAG.24: 1 residues within 4Å: Chain E: N.27 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.27 NAG.31: 5 residues within 4Å: Chain F: E.147, E.150, S.151, N.154, T.156 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:E.147, F:T.156 Water bridges: F:N.154 NAG.38: 2 residues within 4Å: Chain I: N.15 Chain J: Q.15 3 PLIP interactions: 2 interactions with chain J, 1 interactions with chain I Hydrogen bonds: J:Q.15, I:N.15 Water bridges: J:Q.15 NAG.40: 1 residues within 4Å: Chain I: N.27 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:N.27 NAG.47: 5 residues within 4Å: Chain J: E.147, E.150, S.151, N.154, T.156 3 PLIP interactions: 3 interactions with chain J Hydrogen bonds: J:E.147, J:T.156 Water bridges: J:N.154

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 4 residues within 4Å: Chain B: W.14, N.135, C.137 Ligands: EDO.10 1 PLIP interactions: 1 interactions with chain B Water bridges: B:N.135 GOL.25: 4 residues within 4Å: Chain F: W.14, N.135, C.137 Ligands: EDO.26 1 PLIP interactions: 1 interactions with chain F Water bridges: F:N.135 GOL.41: 4 residues within 4Å: Chain J: W.14, N.135, C.137 Ligands: EDO.42 1 PLIP interactions: 1 interactions with chain J Water bridges: J:N.135

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dreyfus, C. et al., Highly conserved protective epitopes on influenza B viruses. Science (2012)

Release Date

2012-08-22

Peptides

Hemagglutinin HA1: AEI
Hemagglutinin HA2: BFJ
antibody CR9114 heavy chain: CGK
antibody CR9114 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

Hemagglutinin HA2

antibody CR9114 heavy chain

antibody CR9114 light chain

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