SMTL ID : 4hlz.1

Crystal Structure of Fab C179 in Complex with a H2N2 influenza virus hemagglutinin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

hetero-3-3-3-3-mer

Ligands

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(Post Translational Modification)(Non-functional Binders)

NAG-NAG-BMA.1: 8 residues within 4Å: Chain A: K.278, N.287 Chain G: G.23, T.24, S.77, Q.78, S.79, I.80 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:Q.78, G:Q.78, G:Q.78 NAG-NAG-BMA.4: 5 residues within 4Å: Chain E: N.287 Chain K: G.23, T.24, Q.78, I.80 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:Q.78

1 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.2: 7 residues within 4Å: Chain C: E.276, N.287 Chain I: G.23, T.24, S.77, Q.78, I.80 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:Q.78, I:Q.78, I:Q.78

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.3: 3 residues within 4Å: Chain C: N.166, W.237, T.239 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 1 residues within 4Å: Chain E: N.13 No protein-ligand interaction detected (PLIP)

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

NAG.6: 3 residues within 4Å: Chain A: N.166, W.237, T.239 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.237, A:T.239 NAG.7: 1 residues within 4Å: Chain A: N.13 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.13 NAG.9: 3 residues within 4Å: Chain B: E.147, N.154, T.156 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.147, B:N.154, B:T.156 NAG.11: 3 residues within 4Å: Chain E: N.166, W.237, T.239 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:W.237, E:T.239 NAG.14: 4 residues within 4Å: Chain F: E.147, S.151, N.154, T.156 3 PLIP interactions: 3 interactions with chain F Hydrophobic interactions: F:T.156 Hydrogen bonds: F:E.147, F:N.154

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

SO4.8: 6 residues within 4Å: Chain B: A.36, D.37, K.38, E.39 Chain H: T.31, A.50 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain H Hydrogen bonds: B:A.36, B:K.38, B:E.39, H:T.31 Salt bridges: B:K.38 SO4.10: 6 residues within 4Å: Chain D: A.36, D.37, K.38, E.39 Chain J: T.31, A.50 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:K.38, D:E.39 Salt bridges: D:K.38 SO4.12: 3 residues within 4Å: Chain E: N.40, K.42, C.275 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.40 Salt bridges: E:K.42 SO4.13: 5 residues within 4Å: Chain F: A.36, D.37, K.38, E.39 Chain L: T.31 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain L Hydrogen bonds: F:K.38, F:E.39, L:T.31 Salt bridges: F:K.38 SO4.15: 3 residues within 4Å: Chain B: A.35 Chain H: W.32, Y.92 3 PLIP interactions: 2 interactions with chain H, 1 interactions with chain B Hydrogen bonds: H:W.32, H:Y.92 Salt bridges: B:K.38 SO4.16: 4 residues within 4Å: Chain D: Y.34, A.35 Chain J: W.32, Y.92 No protein-ligand interaction detected (PLIP) SO4.18: 4 residues within 4Å: Chain F: A.35, K.153 Chain L: W.32, Y.92 1 PLIP interactions: 1 interactions with chain F Salt bridges: F:K.153

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

EDO.17: 3 residues within 4Å: Chain J: P.8, A.9, S.10 3 PLIP interactions: 3 interactions with chain J Hydrogen bonds: J:A.9, J:S.10, J:S.10

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dreyfus, C. et al., Structure of a classical broadly neutralizing stem antibody in complex with a pandemic h2 influenza virus hemagglutinin. J.Virol. (2013)

Release Date

2013-04-17

Peptides

Hemagglutinin HA1: ACE
Hemagglutinin HA2: BDF
Fab C179 heavy chain: GIK
Fab C179 light chain: HJL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

B
B

D
D

F
F

G
G

I
I

K
K

H
H

J
J

L
L

Hemagglutinin HA1

Hemagglutinin HA2

Fab C179 heavy chain

Fab C179 light chain

Related Entries With Identical Sequence