SMTL ID : 4qnp.1

Crystal structure of the 2009 pandemic H1N1 influenza virus neuraminidase with a neutralizing antibody

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

hetero-8-8-8-mer

Ligands

8 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: 4 residues within 4Å: Chain A: N.154, Q.227 Ligands: NAG-NAG.31, NAG-NAG.31 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain B: N.154, Q.227 Ligands: NAG-NAG.12, NAG-NAG.12 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain G: N.154, Q.227 Ligands: NAG-NAG.21, NAG-NAG.21 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain H: N.154, Q.227 Ligands: NAG-NAG.2, NAG-NAG.2 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 4 residues within 4Å: Chain M: N.154, Q.227 Ligands: NAG-NAG.11, NAG-NAG.11 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 4 residues within 4Å: Chain N: N.154, Q.227 Ligands: NAG-NAG.32, NAG-NAG.32 No protein-ligand interaction detected (PLIP) NAG-NAG.31: 4 residues within 4Å: Chain S: N.154, Q.227 Ligands: NAG-NAG.1, NAG-NAG.1 No protein-ligand interaction detected (PLIP) NAG-NAG.32: 4 residues within 4Å: Chain T: N.154, Q.227 Ligands: NAG-NAG.22, NAG-NAG.22 No protein-ligand interaction detected (PLIP)

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

NAG.3: 2 residues within 4Å: Chain A: N.65, T.67 Ligand excluded by PLIP NAG.4: 2 residues within 4Å: Chain A: N.7, S.8 Ligand excluded by PLIP NAG.7: 4 residues within 4Å: Chain B: K.62, N.65, T.67, I.355 Ligand excluded by PLIP NAG.8: 2 residues within 4Å: Chain B: N.7, S.8 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain G: N.65, T.67 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain G: N.7, S.8 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain H: K.62, N.65, T.67, I.355 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain H: N.7, S.8 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain M: N.65, T.67 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain M: N.7, S.8 Ligand excluded by PLIP NAG.27: 4 residues within 4Å: Chain N: K.62, N.65, T.67, I.355 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain N: N.7, S.8 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain S: N.65, T.67 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain S: N.7, S.8 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain T: K.62, N.65, T.67, I.355 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain T: N.7, S.8 Ligand excluded by PLIP

16 x CA: CALCIUM ION(Non-covalent)

CA.5: 5 residues within 4Å: Chain A: D.213, G.217, D.243, G.261, N.263 6 PLIP interactions: 5 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.213, A:G.217, A:D.243, A:G.261, A:N.263, H2O.2 CA.6: 4 residues within 4Å: Chain A: D.295, N.297, D.303, N.305 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.295, A:D.295, A:D.303, A:N.305 CA.9: 5 residues within 4Å: Chain B: D.213, G.217, D.243, G.261, N.263 6 PLIP interactions: 5 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.213, B:G.217, B:D.243, B:G.261, B:N.263, H2O.2 CA.10: 4 residues within 4Å: Chain B: D.295, N.297, D.303, N.305 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.295, B:D.295, B:D.303, B:N.305 CA.15: 5 residues within 4Å: Chain G: D.213, G.217, D.243, G.261, N.263 6 PLIP interactions: 5 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:D.213, G:G.217, G:D.243, G:G.261, G:N.263, H2O.9 CA.16: 4 residues within 4Å: Chain G: D.295, N.297, D.303, N.305 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:D.295, G:D.295, G:D.303, G:N.305 CA.19: 5 residues within 4Å: Chain H: D.213, G.217, D.243, G.261, N.263 6 PLIP interactions: 5 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:D.213, H:G.217, H:D.243, H:G.261, H:N.263, H2O.9 CA.20: 4 residues within 4Å: Chain H: D.295, N.297, D.303, N.305 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:D.295, H:D.295, H:D.303, H:N.305 CA.25: 5 residues within 4Å: Chain M: D.213, G.217, D.243, G.261, N.263 6 PLIP interactions: 5 interactions with chain M, 1 Ligand-Water interactions Metal complexes: M:D.213, M:G.217, M:D.243, M:G.261, M:N.263, H2O.16 CA.26: 4 residues within 4Å: Chain M: D.295, N.297, D.303, N.305 4 PLIP interactions: 4 interactions with chain M Metal complexes: M:D.295, M:D.295, M:D.303, M:N.305 CA.29: 5 residues within 4Å: Chain N: D.213, G.217, D.243, G.261, N.263 6 PLIP interactions: 5 interactions with chain N, 1 Ligand-Water interactions Metal complexes: N:D.213, N:G.217, N:D.243, N:G.261, N:N.263, H2O.16 CA.30: 4 residues within 4Å: Chain N: D.295, N.297, D.303, N.305 4 PLIP interactions: 4 interactions with chain N Metal complexes: N:D.295, N:D.295, N:D.303, N:N.305 CA.35: 5 residues within 4Å: Chain S: D.213, G.217, D.243, G.261, N.263 6 PLIP interactions: 5 interactions with chain S, 1 Ligand-Water interactions Metal complexes: S:D.213, S:G.217, S:D.243, S:G.261, S:N.263, H2O.23 CA.36: 4 residues within 4Å: Chain S: D.295, N.297, D.303, N.305 4 PLIP interactions: 4 interactions with chain S Metal complexes: S:D.295, S:D.295, S:D.303, S:N.305 CA.39: 5 residues within 4Å: Chain T: D.213, G.217, D.243, G.261, N.263 6 PLIP interactions: 5 interactions with chain T, 1 Ligand-Water interactions Metal complexes: T:D.213, T:G.217, T:D.243, T:G.261, T:N.263, H2O.23 CA.40: 4 residues within 4Å: Chain T: D.295, N.297, D.303, N.305 4 PLIP interactions: 4 interactions with chain T Metal complexes: T:D.295, T:D.295, T:D.303, T:N.305

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wan, H. et al., Structural characterization of a protective epitope spanning A(H1N1)pdm09 influenza virus neuraminidase monomers. Nat Commun (2015)

Release Date

2015-02-11

Peptides

Neuraminidase: ABGHMNST
neutralizing antibody, light chain: CEIKOQUW
neutralizing antibody, heavy chain: DFJLPRVX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

G
A

H
B

M
A

N
B

S
A

T
B

C
F

E
L

I
F

K
L

O
F

Q
L

U
F

W
L

D
E

F
H

J
E

L
H

P
E

R
H

V
E

X
H

Neuraminidase

neutralizing antibody, light chain

neutralizing antibody, heavy chain