6ATY | pdb_00006aty

Exploring Cystine Dense Peptide Space to Open a Unique Molecular Toolbox

PDB DOI: https://doi.org/10.2210/pdb6ATY/pdb

Classification: TOXIN
Organism(s): Lychas mucronatus
Expression System: Homo sapiens
Mutation(s): No
Membrane Protein: Yes OPM

Deposited: 2017-08-29 Released: 2018-08-22
Deposition Author(s): Gewe, M.M., Rupert, P., Strong, R.K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.223 (Depositor), 0.220 (DCC)
R-Value Work:
0.166 (Depositor), 0.170 (DCC)
R-Value Observed:
0.169 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Exploring Cystine Dense Peptide Space to Open a Unique Molecular Toolbox

Correnti, C., Gewe, M.M.

To be published.

Macromolecule Content

Total Structure Weight: 4.24 kDa
Atom Count: 331
Modeled Residue Count: 38
Deposited Residue Count: 39
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Venom protein 51.1	A	39	Lychas mucronatus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P0CJ17 (Lychas mucronatus) Explore P0CJ17 Go to UniProtKB: P0CJ17
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0CJ17
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.223 (Depositor), 0.220 (DCC)
R-Value Work: 0.166 (Depositor), 0.170 (DCC)
R-Value Observed: 0.169 (Depositor)

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.775	α = 90
b = 39.775	β = 90
c = 68.563	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2018-08-22

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-08-22
Type: Initial release
Version 1.1: 2024-11-13
Changes: Data collection, Database references, Structure summary

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.