SMTL ID : 7bud.3 (3 other biounits)

Cryo-EM structure of Dengue virus serotype 2 complexed with Fab SIgN-3C at pH 8.0

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-12-12-18-18-mer

Ligands

18 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 C: N.149, N.153, T.155 Chain U: R.112 1 PLIP interactions: 1 interactions with chain U Hydrogen bonds: U:R.112 NAG-NAG.2: 5 residues within 4Å: Chain E: N.149, N.153, T.155 Chain G: W.101, G.102 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain G: N.149, N.153, T.155 Chain I: R.112 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain M: N.149, N.153, T.155 Chain e: R.112 1 PLIP interactions: 1 interactions with chain e Hydrogen bonds: e:R.112 NAG-NAG.8: 5 residues within 4Å: Chain O: N.149, N.153, T.155 Chain Q: W.101, G.102 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain Q: N.149, N.153, T.155 Chain S: R.112 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain A: R.112 Chain W: N.149, N.153, T.155 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.112 NAG-NAG.14: 5 residues within 4Å: Chain 0: W.101, G.102 Chain Y: N.149, N.153, T.155 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 4 residues within 4Å: Chain 0: N.149, N.153, T.155 Chain 2: R.112 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 4 residues within 4Å: Chain 6: N.149, N.153, T.155 Chain o: R.112 1 PLIP interactions: 1 interactions with chain o Hydrogen bonds: o:R.112 NAG-NAG.20: 5 residues within 4Å: Chain 8: N.149, N.153, T.155 Chain a: W.101, G.102 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 4 residues within 4Å: Chain a: N.149, N.153, T.155 Chain c: R.112 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 4 residues within 4Å: Chain K: R.112 Chain g: N.149, N.153, T.155 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:R.112 NAG-NAG.26: 5 residues within 4Å: Chain i: N.149, N.153, T.155 Chain k: W.101, G.102 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 4 residues within 4Å: Chain k: N.149, N.153, T.155 Chain m: R.112 No protein-ligand interaction detected (PLIP) NAG-NAG.31: 4 residues within 4Å: Chain 4: R.112 Chain q: N.149, N.153, T.155 1 PLIP interactions: 1 interactions with chain 4 Hydrogen bonds: 4:R.112 NAG-NAG.32: 5 residues within 4Å: Chain s: N.149, N.153, T.155 Chain u: W.101, G.102 No protein-ligand interaction detected (PLIP) NAG-NAG.33: 4 residues within 4Å: Chain u: N.149, N.153, T.155 Chain w: R.112 No protein-ligand interaction detected (PLIP)

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

NAG.4: 3 residues within 4Å: Chain A: D.73 Chain C: N.67, M.118 Ligand excluded by PLIP NAG.5: 2 residues within 4Å: Chain E: N.67 Chain I: D.73 Ligand excluded by PLIP NAG.6: 2 residues within 4Å: Chain G: T.66, N.67 Ligand excluded by PLIP NAG.10: 3 residues within 4Å: Chain K: D.73 Chain M: N.67, M.118 Ligand excluded by PLIP NAG.11: 2 residues within 4Å: Chain O: N.67 Chain S: D.73 Ligand excluded by PLIP NAG.12: 2 residues within 4Å: Chain Q: T.66, N.67 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain U: D.73 Chain W: N.67, M.118 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain 2: D.73 Chain Y: N.67 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain 0: T.66, N.67 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain 4: D.73 Chain 6: N.67, M.118 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain 8: N.67 Chain c: D.73 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain a: T.66, N.67 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain e: D.73 Chain g: N.67, M.118 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain i: N.67 Chain m: D.73 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain k: T.66, N.67 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain o: D.73 Chain q: N.67, M.118 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain s: N.67 Chain w: D.73 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain u: T.66, N.67 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, S. et al., A Human Antibody Neutralizes Different Flaviviruses by Using Different Mechanisms. Cell Rep (2020)

Release Date

2020-05-13

Peptides

SIgN-3C Fab heavy chain: AIKSU24cemow
SIgN-3C Fab light chain: BJLTV35dfnpx
Dengue virus serotype 2 E protein: CEGMOQWY068agikqsu
Dengue virus serotype 2 M protein: DFHNPRXZ179bhjlrtv

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

I
H

K
G

S
H

U
G

2
H

4
G

c
H

e
G

m
H

o
G

w
H

B
I

J
L

L
I

T
L

V
I

3
L

5
I

d
L

f
I

n
L

p
I

x
L

C
B

E
A

G
C

M
B

O
A

Q
C

W
B

Y
A

0
C

6
B

8
A

a
C

g
B

i
A

k
C

q
B

s
A

u
C

D
E

F
D

H
F

N
E

P
D

R
F

X
E

Z
D

1
F

7
E

9
D

b
F

h
E

j
D

l
F

r
E

t
D

v
F

SIgN-3C Fab heavy chain

SIgN-3C Fab light chain

Dengue virus serotype 2 E protein

Dengue virus serotype 2 M protein

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