4BZ2 | pdb_00004bz2

Structure of dengue virus EDIII in complex with Fab 2D73

PDB DOI: https://doi.org/10.2210/pdb4BZ2/pdb

Classification: IMMUNE SYSTEM-VIRAL PROTEIN COMPLEX
Organism(s): dengue virus type 4, Mus musculus
Expression System: Komagataella phaffii GS115
Mutation(s): No

Deposited: 2013-07-23 Released: 2014-08-13
Deposition Author(s): Li, J., Watterson, D., Chang, C.W., Li, X.Q., Ericsson, D.J., Qiu, L.W., Cai, J.P., Chen, J., Fry, S.R., Cooper, M.A., Che, X.Y., Young, P.R., Kobe, B.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.03 Å
R-Value Free:
0.225 (Depositor), 0.237 (DCC)
R-Value Work:
0.205 (Depositor), 0.218 (DCC)
R-Value Observed:
0.206 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Structure of Dengue Virus Ediii in Complex with Fab 2D73

Li, J., Watterson, D., Chang, C.W., Li, X.Q., Ericsson, D.J., Qiu, L.W., Cai, J.P., Chen, J., Fry, S.R., Cooper, M.A., Che, X.Y., Young, P.R., Kobe, B.

To be published.

Macromolecule Content

Total Structure Weight: 59.53 kDa
Atom Count: 4,233
Modeled Residue Count: 526
Deposited Residue Count: 534
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ENVELOPE PROTEIN	A	101	dengue virus type 4	Mutation(s): 0
UniProt
Find proteins for Q7TGC7 (Dengue virus type 4) Explore Q7TGC7 Go to UniProtKB: Q7TGC7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7TGC7
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
FAB 2D73 HEAVY CHAIN	B [auth H]	221	Mus musculus	Mutation(s): 0

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
FAB 2D73 LIGHT CHAIN	C [auth L]	212	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain K [auth H] MOL2 format, chain K [auth H] mmCIF format, chain K [auth H]	K [auth H]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain K [auth H] Interactions & Density Focus chain K [auth H]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain L [auth H] SDF format, chain M [auth H] SDF format, chain R [auth L] MOL2 format, chain L [auth H] MOL2 format, chain M [auth H] MOL2 format, chain R [auth L] mmCIF format, chain L [auth H] mmCIF format, chain M [auth H] mmCIF format, chain R [auth L]	L [auth H], M [auth H], R [auth L]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain L [auth H] Focus chain M [auth H] Focus chain R [auth L] Interactions & Density Focus chain L [auth H] Focus chain M [auth H] Focus chain R [auth L]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain H SDF format, chain N [auth L] SDF format, chain O [auth L] MOL2 format, chain H MOL2 format, chain N [auth L] MOL2 format, chain O [auth L] mmCIF format, chain H mmCIF format, chain N [auth L] mmCIF format, chain O [auth L]	H, N [auth L], O [auth L]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H Focus chain N [auth L] Focus chain O [auth L] Interactions & Density Focus chain H Focus chain N [auth L] Focus chain O [auth L]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth H] SDF format, chain J [auth H] SDF format, chain Q [auth L] SDF format, chain P [auth L] SDF format, chain I [auth H] SDF format, chain F [auth A] SDF format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain G [auth H] MOL2 format, chain J [auth H] MOL2 format, chain Q [auth L] MOL2 format, chain P [auth L] MOL2 format, chain I [auth H] MOL2 format, chain F [auth A] MOL2 format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain G [auth H] mmCIF format, chain J [auth H] mmCIF format, chain Q [auth L] mmCIF format, chain P [auth L] mmCIF format, chain I [auth H] mmCIF format, chain F [auth A] mmCIF format, chain D [auth A]	D [auth A] E [auth A] F [auth A] G [auth H] I [auth H] D [auth A], E [auth A], F [auth A], G [auth H], I [auth H], J [auth H], P [auth L], Q [auth L]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth H] Focus chain I [auth H] Focus chain J [auth H] Focus chain P [auth L] Focus chain Q [auth L] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth H] Focus chain I [auth H] Focus chain J [auth H] Focus chain P [auth L] Focus chain Q [auth L]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.03 Å
R-Value Free: 0.225 (Depositor), 0.237 (DCC)
R-Value Work: 0.205 (Depositor), 0.218 (DCC)
R-Value Observed: 0.206 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.655	α = 90
b = 108.655	β = 90
c = 108.564	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2014-08-13

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-08-13
Type: Initial release
Version 1.1: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description
Version 1.2: 2024-10-23
Changes: Structure summary