SMTL ID : 6xpx.1

Human antibody S1V2-51 in complex with the influenza hemagglutinin head domain of A/Aichi/2/1968 (X-31)(H3N2)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 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

NAG-NAG-BMA.1: 4 residues within 4Å: Chain A: S.9, N.249, N.260, V.261 No protein-ligand interaction detected (PLIP)

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

NAG.2: 2 residues within 4Å: Chain A: N.129, N.210 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.129 NAG.3: 3 residues within 4Å: Chain A: Q.44, N.45, F.84 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.45

2 x BCN: BICINE(Non-covalent)

BCN.4: 5 residues within 4Å: Chain A: S.59, Y.64, D.65, V.66, Y.69 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.59, A:V.66, A:V.66 Water bridges: A:Y.69 BCN.7: 4 residues within 4Å: Chain A: G.88, T.90, V.130, T.131 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.90

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 3 residues within 4Å: Chain A: R.21, I.22, L.23 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.46 GOL.6: 3 residues within 4Å: Chain A: I.26, D.27, H.39 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.26, A:D.27 GOL.8: 6 residues within 4Å: Chain A: D.65, H.148, N.180, R.184, R.193 Chain C: E.57 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:H.148, A:N.180, A:R.184, C:E.57 Water bridges: C:E.57 GOL.10: 5 residues within 4Å: Chain B: G.72, S.73, G.74, T.75, D.76 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.73, B:T.75, B:T.75, B:D.76, B:D.76 GOL.11: 3 residues within 4Å: Chain B: F.104, Q.106 Chain C: L.45 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:F.104 GOL.12: 11 residues within 4Å: Chain B: Q.166, S.168, S.182, S.183, T.184 Chain C: F.169, P.170, V.172, S.180, L.181, S.182 6 PLIP interactions: 2 interactions with chain C, 4 interactions with chain B Hydrogen bonds: C:P.170, C:S.182, B:S.168, B:S.183, B:T.184, B:T.184 GOL.13: 6 residues within 4Å: Chain B: T.170, D.173, S.174 Chain C: V.166, H.167, T.168 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:H.167, C:T.168, B:S.174, B:S.174

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.9: 5 residues within 4Å: Chain A: L.190 Chain B: D.35, K.36, Y.38, W.56 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

McCarthy, K.R. et al., A Prevalent Focused Human Antibody Response to the Influenza Virus Hemagglutinin Head Interface. Mbio (2021)

Release Date

2021-05-19

Peptides

Hemagglutinin: A
S1V2-51 Fab light chain: B
S1V2-51 Fab heavy chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
B

Hemagglutinin

S1V2-51 Fab light chain

S1V2-51 Fab heavy chain