SMTL ID : 7a3t.1

Crystal structure of dengue 3 virus envelope glycoprotein in complex with the Fab fragment of the broadly neutralizing human antibody EDE1 C8

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

hetero-2-2-2-mer

Ligands

2 x NAG- NAG- BMA- MAN- FUC: alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-FUC.1: 3 residues within 4Å: Chain A: T.66, N.67 Ligands: GOL.5 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-FUC.7: 3 residues within 4Å: Chain B: T.66, N.67 Ligands: GOL.11 No protein-ligand interaction detected (PLIP)

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

SO4.2: 6 residues within 4Å: Chain A: C.74, T.76, Q.77, C.105, G.106, C.107 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.76, A:T.76, A:T.76, A:G.106, A:C.107 SO4.3: 5 residues within 4Å: Chain A: R.232, E.233 Chain D: K.152, N.155, L.157 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:E.233, A:E.233 Salt bridges: A:R.232, D:K.152 SO4.8: 6 residues within 4Å: Chain B: C.74, T.76, Q.77, C.105, G.106, C.107 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.76, B:T.76, B:T.76, B:G.106, B:C.107 SO4.9: 5 residues within 4Å: Chain B: R.232, E.233 Chain F: K.152, N.155, L.157 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain F Hydrogen bonds: B:E.233 Salt bridges: B:R.232, F:K.152 SO4.13: 6 residues within 4Å: Chain C: G.53, E.54, S.101, N.102, F.103, Y.104 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:G.53, C:E.54, C:Y.104 SO4.14: 10 residues within 4Å: Chain C: F.175, P.176, V.178, S.186, L.187, S.188 Chain D: Q.163, S.165, S.179, T.181 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:S.165, D:S.179, C:S.188, C:S.188 SO4.16: 6 residues within 4Å: Chain E: G.53, E.54, S.101, N.102, F.103, Y.104 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:G.53, E:E.54, E:Y.104 SO4.17: 10 residues within 4Å: Chain E: F.175, P.176, V.178, S.186, L.187, S.188 Chain F: Q.163, S.165, S.179, T.181 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:S.188, E:S.188, F:S.165, F:S.179

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 1 residues within 4Å: Chain A: R.73 No protein-ligand interaction detected (PLIP) GOL.5: 3 residues within 4Å: Chain A: N.67, I.68 Ligands: NAG-NAG-BMA-MAN-FUC.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.68, A:I.68 GOL.6: 4 residues within 4Å: Chain A: K.58, C.121, L.122, S.124 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.124, A:S.124 GOL.10: 1 residues within 4Å: Chain B: R.73 No protein-ligand interaction detected (PLIP) GOL.11: 3 residues within 4Å: Chain B: N.67, I.68 Ligands: NAG-NAG-BMA-MAN-FUC.7 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:I.68, B:I.68 GOL.12: 4 residues within 4Å: Chain B: K.58, C.121, L.122, S.124 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.124, B:S.124 GOL.15: 7 residues within 4Å: Chain C: V.172, H.173 Chain D: T.167, E.168, Q.169, D.170, S.171 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:E.168, D:S.171, C:V.172, C:T.174 GOL.18: 7 residues within 4Å: Chain E: V.172, H.173 Chain F: T.167, E.168, Q.169, D.170, S.171 7 PLIP interactions: 3 interactions with chain E, 4 interactions with chain F Hydrogen bonds: E:V.172, E:H.173, E:T.174, F:T.167, F:E.168, F:D.170, F:S.171

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sharma, A. et al., The epitope arrangement on flavivirus particles contributes to Mab C10's extraordinary neutralization breadth across Zika and dengue viruses. Cell (2021)

Release Date

2021-12-08

Peptides

Core protein: AB
EDE1 C8 antibody Fab fragment: CE
EDE1 C8 antibody Fab fragment: DF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
H

E
H

D
L

F
L

Core protein

EDE1 C8 antibody Fab fragment

EDE1 C8 antibody Fab fragment

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