6R5M | pdb_00006r5m

Crystal structure of toxin MT9 from mamba venom

PDB DOI: https://doi.org/10.2210/pdb6R5M/pdb
Entry: 6R5M supersedes: 6F21

Classification: TOXIN
Organism(s): Dendroaspis polylepis
Mutation(s): No

Deposited: 2019-03-25 Released: 2020-02-12
Deposition Author(s): Stura, E.A., Tepshi, L., Ciolek, J., Triquigneaux, M., Zoukimian, C., De Waard, M., Beroud, R., Servent, D., Gilles, N., Legrand, P., Ciccone, L.
Funding Organization(s): French National Research Agency

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.251 (Depositor), 0.273 (DCC)
R-Value Work:
0.231 (Depositor), 0.242 (DCC)
R-Value Observed:
0.232 (Depositor)

wwPDB Validation 3D Report Full Report

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

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 6F21

Literature

MT9, a natural peptide from black mamba venom antagonizes the muscarinic type 2 receptor and reverses the M2R-agonist-induced relaxation in rat and human arteries

Ciolek, J., Zoukimian, C., Dhot, J., Burban, M., Triquigneaux, M., Lauzier, B., Guimbert, C., Boturyn, D., Ferron, M., Ciccone, L., Tepshi, L., Stura, E., Legrand, P., Robin, P., Mourier, G., Schaack, B., Fellah, I., Blanchet, G., Gauthier-Erfanian, C., Beroud, R., Servent, D., De Waard, M., Gilles, N.

(2022) Biomed Pharmacother 150: 113094

DOI: https://doi.org/10.1016/j.biopha.2022.113094

Macromolecule Content

Total Structure Weight: 20.28 kDa
Atom Count: 1,554
Modeled Residue Count: 171
Deposited Residue Count: 171
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dendroaspis polylepis MT9	A, B, C	57	Dendroaspis polylepis	Mutation(s): 0
UniProt
Find proteins for A0A4P1LYC9 (Dendroaspis polylepis polylepis) Explore A0A4P1LYC9 Go to UniProtKB: A0A4P1LYC9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A4P1LYC9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain P [auth C] SDF format, chain O [auth C] SDF format, chain N [auth C] SDF format, chain M [auth C] SDF format, chain L [auth C] SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain P [auth C] MOL2 format, chain O [auth C] MOL2 format, chain N [auth C] MOL2 format, chain M [auth C] MOL2 format, chain L [auth C] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain P [auth C] mmCIF format, chain O [auth C] mmCIF format, chain N [auth C] mmCIF format, chain M [auth C] mmCIF format, chain L [auth C] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A] E [auth A] H [auth B] I [auth B] L [auth C] D [auth A], E [auth A], H [auth B], I [auth B], L [auth C], M [auth C], N [auth C], O [auth C], P [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C]
GOL Query on GOL 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]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [auth B]
PGO Query on PGO Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A], G [auth A]	S-1,2-PROPANEDIOL C₃ H₈ O₂ DNIAPMSPPWPWGF-VKHMYHEASA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A]
ACE Query on ACE Download:Ideal Coordinates CCD File SDF format, chain K [auth C] MOL2 format, chain K [auth C] mmCIF format, chain K [auth C]	K [auth C]	ACETYL GROUP C₂ H₄ O IKHGUXGNUITLKF-UHFFFAOYSA-N		Interactions Focus chain K [auth C] Interactions & Density Focus chain K [auth C]