SMTL ID : 4bz2.1

Structure of dengue virus EDIII in complex with Fab 2D73

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.03 Å

Oligo State

hetero-1-1-1-mer

Ligands

8 x NA: SODIUM ION(Non-functional Binders)

NA.1: 6 residues within 4Å: Chain A: P.41, I.42, E.43, V.84, I.85, G.86 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.41, A:E.43 Water bridges: A:R.45 NA.2: 3 residues within 4Å: Chain A: E.43, R.45, V.52 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.43, A:R.45 NA.3: 7 residues within 4Å: Chain A: E.19, G.23, T.24, T.25, P.76, W.96, R.98 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.23 Water bridges: A:E.19 NA.4: 5 residues within 4Å: Chain B: Q.39, G.42, K.43 Chain C: Y.87 Ligands: CL.5 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.39, B:G.42 NA.6: 4 residues within 4Å: Chain B: K.38, Q.39, S.40, E.46 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.40, B:S.40, B:E.46 NA.7: 6 residues within 4Å: Chain B: S.7, G.8, P.9, Q.113, G.114, T.115 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.7, B:Q.113 NA.13: 2 residues within 4Å: Chain C: Q.69, D.70 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.70 Water bridges: C:Q.69 NA.14: 4 residues within 4Å: Chain C: S.60, R.61, S.63, S.76 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.61 Water bridges: C:S.76

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

CL.5: 7 residues within 4Å: Chain B: Q.39, S.40, H.41, G.42, K.43 Ligands: NA.4, CL.12 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain C: Q.37, K.39, E.81 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain C: P.40, G.41 Ligands: CL.5 Ligand excluded by PLIP

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.8: 15 residues within 4Å: Chain A: K.15, A.18, E.19, Q.21, V.26 Chain B: R.99, G.100, Y.101, R.102, Y.103, G.105, H.107 Chain C: D.32, R.50, Y.91 7 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: B:R.99, B:R.99, B:G.105, B:G.105, B:H.107, A:K.15, C:D.32

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 5 residues within 4Å: Chain C: M.11, A.13, E.17, R.18, V.19 No protein-ligand interaction detected (PLIP) GOL.10: 5 residues within 4Å: Chain B: S.25, G.26, Y.27, T.28, R.77 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.26 GOL.15: 5 residues within 4Å: Chain C: T.5, Q.6, S.7, P.8, S.9 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.6, C:S.9

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, J. et al., Structure of Dengue Virus Ediii in Complex with Fab 2D73. To be Published

Release Date

2014-08-13

Peptides

ENVELOPE PROTEIN: A
FAB 2D73 HEAVY CHAIN: B
FAB 2D73 LIGHT CHAIN: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
H

C
L

ENVELOPE PROTEIN

FAB 2D73 HEAVY CHAIN

FAB 2D73 LIGHT CHAIN