SMTL ID : 3gbm.1 (1 other biounit)

Crystal Structure of Fab CR6261 in Complex with a H5N1 influenza virus hemagglutinin.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 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 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 5 residues within 4Å: Chain A: S.221 Chain E: N.169, N.240, D.241, A.242 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 5 residues within 4Å: Chain E: S.221 Chain I: N.169, N.240, D.241, A.242 No protein-ligand interaction detected (PLIP)

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

NAG.2: 1 residues within 4Å: Chain A: N.27 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.27 NAG.4: 1 residues within 4Å: Chain A: N.158 No protein-ligand interaction detected (PLIP) NAG.6: 4 residues within 4Å: Chain B: E.147, E.150, N.154 Chain D: Y.33 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.147, B:E.150, B:N.154 NAG.9: 1 residues within 4Å: Chain E: N.27 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.27 NAG.11: 1 residues within 4Å: Chain E: N.158 No protein-ligand interaction detected (PLIP) NAG.13: 4 residues within 4Å: Chain F: E.147, E.150, N.154 Chain H: Y.33 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:E.147, F:E.150, F:N.154 NAG.16: 1 residues within 4Å: Chain I: N.27 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:N.27 NAG.18: 1 residues within 4Å: Chain I: N.158 No protein-ligand interaction detected (PLIP) NAG.20: 4 residues within 4Å: Chain J: E.147, E.150, N.154 Chain L: Y.33 3 PLIP interactions: 2 interactions with chain J, 1 interactions with chain L Hydrogen bonds: J:E.147, J:N.154, L:Y.33

3 x BMA: beta-D-mannopyranose(Non-functional Binders)

BMA.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) BMA.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) BMA.17: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

EDO.5: 7 residues within 4Å: Chain A: V.20, D.21, R.314, L.315, V.316 Chain B: V.100, N.104 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:N.104, A:D.21, A:R.314 EDO.12: 7 residues within 4Å: Chain E: V.20, D.21, R.314, L.315, V.316 Chain F: V.100, N.104 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:D.21, E:R.314, F:N.104 EDO.19: 7 residues within 4Å: Chain I: V.20, D.21, R.314, L.315, V.316 Chain J: V.100, N.104 3 PLIP interactions: 2 interactions with chain I, 1 interactions with chain J Hydrogen bonds: I:D.21, I:R.314, J:N.104

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 7 residues within 4Å: Chain B: A.36, D.37, K.38, E.39, E.150, R.153, N.154 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.37, B:K.38, B:E.39, B:E.39, B:E.150 GOL.14: 7 residues within 4Å: Chain F: A.36, D.37, K.38, E.39, E.150, R.153, N.154 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:D.37, F:K.38, F:E.39, F:E.39, F:E.150 GOL.21: 7 residues within 4Å: Chain J: A.36, D.37, K.38, E.39, E.150, R.153, N.154 5 PLIP interactions: 5 interactions with chain J Hydrogen bonds: J:D.37, J:K.38, J:E.39, J:E.39, J:E.150

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ekiert, D.C. et al., Antibody recognition of a highly conserved influenza virus epitope. Science (2009)

Release Date

2009-03-10

Peptides

Hemagglutinin: AEI
Hemagglutinin: BFJ
antibody (Fab): CGK
antibody (Fab): 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

Hemagglutinin

antibody (Fab)

antibody (Fab)

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