SMTL ID : 5w6g.1

Human antibody 6649 in complex with influenza hemagglutinin H1 Solomon Islands

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.79 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: 8 residues within 4Å: Chain A: N.72, E.74, E.94, N.95, C.98, S.142, S.144, R.228 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 8 residues within 4Å: Chain E: N.72, E.74, E.94, N.95, C.98, S.142, S.144, R.228 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 8 residues within 4Å: Chain I: N.72, E.74, E.94, N.95, C.98, S.142, S.144, R.228 No protein-ligand interaction detected (PLIP)

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

NAG.2: 2 residues within 4Å: Chain A: N.62, E.94 No protein-ligand interaction detected (PLIP) NAG.3: 3 residues within 4Å: Chain A: N.133, N.162 Chain D: I.96 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:N.162 Hydrophobic interactions: D:I.96 NAG.4: 3 residues within 4Å: Chain A: N.294, S.296, L.297 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.296 NAG.5: 1 residues within 4Å: Chain A: N.31 No protein-ligand interaction detected (PLIP) NAG.15: 2 residues within 4Å: Chain E: N.62, E.94 No protein-ligand interaction detected (PLIP) NAG.16: 3 residues within 4Å: Chain E: N.133, N.162 Chain H: I.96 2 PLIP interactions: 1 interactions with chain H, 1 interactions with chain E Hydrophobic interactions: H:I.96 Hydrogen bonds: E:N.162 NAG.17: 3 residues within 4Å: Chain E: N.294, S.296, L.297 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:S.296 NAG.18: 1 residues within 4Å: Chain E: N.31 No protein-ligand interaction detected (PLIP) NAG.28: 2 residues within 4Å: Chain I: N.62, E.94 No protein-ligand interaction detected (PLIP) NAG.29: 3 residues within 4Å: Chain I: N.133, N.162 Chain L: I.96 2 PLIP interactions: 1 interactions with chain L, 1 interactions with chain I Hydrophobic interactions: L:I.96 Hydrogen bonds: I:N.162 NAG.30: 3 residues within 4Å: Chain I: N.294, S.296, L.297 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:S.296 NAG.31: 1 residues within 4Å: Chain I: N.31 No protein-ligand interaction detected (PLIP)

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

SO4.6: 3 residues within 4Å: Chain A: K.127, K.153, R.259 Ligand excluded by PLIP SO4.7: 7 residues within 4Å: Chain A: Y.99, P.190, D.194, D.229, R.230, E.231, G.232 Ligand excluded by PLIP SO4.8: 4 residues within 4Å: Chain A: H.200, T.201, E.202, N.203 Ligand excluded by PLIP SO4.9: 7 residues within 4Å: Chain A: G.160, K.161, N.162, G.163, L.164, A.197, H.200 Ligand excluded by PLIP SO4.10: 3 residues within 4Å: Chain A: F.122, E.123 Chain C: N.104 Ligand excluded by PLIP SO4.11: 3 residues within 4Å: Chain A: R.81, E.82, S.83 Ligand excluded by PLIP SO4.19: 3 residues within 4Å: Chain E: K.127, K.153, R.259 Ligand excluded by PLIP SO4.20: 7 residues within 4Å: Chain E: Y.99, P.190, D.194, D.229, R.230, E.231, G.232 Ligand excluded by PLIP SO4.21: 4 residues within 4Å: Chain E: H.200, T.201, E.202, N.203 Ligand excluded by PLIP SO4.22: 7 residues within 4Å: Chain E: G.160, K.161, N.162, G.163, L.164, A.197, H.200 Ligand excluded by PLIP SO4.23: 3 residues within 4Å: Chain E: F.122, E.123 Chain G: N.104 Ligand excluded by PLIP SO4.24: 3 residues within 4Å: Chain E: R.81, E.82, S.83 Ligand excluded by PLIP SO4.32: 3 residues within 4Å: Chain I: K.127, K.153, R.259 Ligand excluded by PLIP SO4.33: 7 residues within 4Å: Chain I: Y.99, P.190, D.194, D.229, R.230, E.231, G.232 Ligand excluded by PLIP SO4.34: 4 residues within 4Å: Chain I: H.200, T.201, E.202, N.203 Ligand excluded by PLIP SO4.35: 7 residues within 4Å: Chain I: G.160, K.161, N.162, G.163, L.164, A.197, H.200 Ligand excluded by PLIP SO4.36: 3 residues within 4Å: Chain I: F.122, E.123 Chain K: N.104 Ligand excluded by PLIP SO4.37: 3 residues within 4Å: Chain I: R.81, E.82, S.83 Ligand excluded by PLIP

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.12: 4 residues within 4Å: Chain A: S.64, G.96, T.97, Y.106 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.64, A:T.97, A:Y.106 GOL.13: 4 residues within 4Å: Chain A: G.101, H.102, F.103 Chain E: H.212 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.103, A:F.103 GOL.25: 4 residues within 4Å: Chain E: S.64, G.96, T.97, Y.106 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:S.64, E:T.97 GOL.26: 4 residues within 4Å: Chain E: G.101, H.102, F.103 Chain I: H.212 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:F.103, E:F.103 GOL.38: 4 residues within 4Å: Chain I: S.64, G.96, T.97, Y.106 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:S.64, I:T.97 GOL.39: 4 residues within 4Å: Chain A: H.212 Chain I: G.101, H.102, F.103 3 PLIP interactions: 3 interactions with chain I Hydrogen bonds: I:H.102, I:F.103, I:F.103

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Raymond, D.D. et al., Conserved epitope on influenza-virus hemagglutinin head defined by a vaccine-induced antibody. Proc. Natl. Acad. Sci. U.S.A. (2018)

Release Date

2017-12-20

Peptides

Hemagglutinin HA1: AEI
Hemagglutinin HA2: BFJ
6649 antibody heavy chain: CGK
6649 antibody 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

6649 antibody heavy chain

6649 antibody light chain

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