SMTL ID : 6flb.1

3H5 Fab bound to EDIII of DenV 2 Xtal form 2

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 5 residues within 4Å: Chain A: K.47, E.86, Q.89, K.91 Chain B: R.59 8 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B, 1 interactions with chain C Hydrogen bonds: A:E.86, A:Q.89 Water bridges: A:Q.89, B:R.59, C:V.98 Salt bridges: A:K.47, A:K.91, B:R.59

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 2 residues within 4Å: Chain B: D.105 Chain C: E.59 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:D.105, B:D.105, C:E.59 Water bridges: B:F.102 GOL.4: 6 residues within 4Å: Chain B: V.167, H.168 Chain C: T.168, D.169, D.171, T.176 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:V.167, C:T.168, C:D.169, C:T.176 Water bridges: C:D.169 GOL.5: 3 residues within 4Å: Chain C: E.189, R.192, H.193 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.189, C:R.192

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 7 residues within 4Å: Chain B: Q.35, K.99, A.103, M.104 Chain C: Q.93, N.95, F.100 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Renner, M. et al., Characterization of a potent and highly unusual minimally enhancing antibody directed against dengue virus. Nat. Immunol. (2018)

Release Date

2018-10-24

Peptides

Domain III of Dengue virus 2: A
Heavy chain of 3H5 Fab: B
Light chain of 3H5 Fab: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

C
L

Domain III of Dengue virus 2

Heavy chain of 3H5 Fab

Light chain of 3H5 Fab

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