5XWE

Structure of a three finger toxin from Ophiophagus hannah venom

PDB DOI: https://doi.org/10.2210/pdb5XWE/pdb

Classification: TOXIN
Organism(s): Ophiophagus hannah
Mutation(s): No

Deposited: 2017-06-29 Released: 2018-07-11
Deposition Author(s): Jobichen, C., Roy, A., Kini, R.M., Sivaraman, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.274 (Depositor), 0.280 (DCC)
R-Value Work:
0.238 (Depositor), 0.250 (DCC)
R-Value Observed:
0.257 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 2.2 of the entry. See complete history.

Literature

Structure of a three finger toxin from Ophiophagus hannah venom

Jobichen, C., Roy, A., Kin, R.M., Sivaraman, J.

To be published.

Macromolecule Content

Total Structure Weight: 19.22 kDa
Atom Count: 849
Modelled Residue Count: 101
Deposited Residue Count: 166
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Weak toxin DE-1 homolog 1	A, B	83	Ophiophagus hannah	Mutation(s): 0
UniProt
Find proteins for Q69CJ8 (Ophiophagus hannah) Explore Q69CJ8 Go to UniProtKB: Q69CJ8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q69CJ8
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain G [auth B] mmCIF format, chain C [auth A] mmCIF format, chain G [auth B]	C [auth A], G [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B] mmCIF format, chain J [auth B]	J [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B]	D [auth A], E [auth A], F [auth A], H [auth B], I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.274 (Depositor), 0.280 (DCC)
R-Value Work: 0.238 (Depositor), 0.250 (DCC)
R-Value Observed: 0.257 (Depositor)

Space Group: P 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.48	α = 90
b = 18.183	β = 104.75
c = 77.19	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2018-07-11

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-07-11
Type: Initial release
Version 2.0: 2021-06-02
Type: Coordinate replacement
Reason: Atoms with unrealistic or zero occupancies
Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Refinement description, Source and taxonomy, Structure summary
Version 2.1: 2023-11-22
Changes: Data collection, Database references, Refinement description
Version 2.2: 2024-11-20
Changes: Structure summary