6VAN

Crystal structure of caltubin from the great pond snail

PDB DOI: https://doi.org/10.2210/pdb6VAN/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Lymnaea stagnalis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-12-17 Released: 2020-12-23
Deposition Author(s): Dong, A., Li, A., Zhang, Q., Barszczyk, A., Chern, Y.H., Arrowsmith, C.H., Edwards, A.M., Zhong, Z.P., Tong, Y., Structural Genomics Consortium (SGC)
Funding Organization(s): Canadian Institutes of Health Research (CIHR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.33 Å
R-Value Free: 0.222
R-Value Work: 0.191
R-Value Observed: 0.192

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Cell-penetrating caltubin promotes neurite outgrowth and regrowth through calcium-dependent microtubule regulation

Dong, A., Li, A., Zhang, Q., Barszczyk, A., Chern, Y.H., Arrowsmith, C.H., Edwards, A.M., Zhong, Z.P., Tong, Y., Structural Genomics Consortium (SGC)

To be published.

Macromolecule Content

Total Structure Weight: 34.47 kDa
Atom Count: 2,820
Modelled Residue Count: 288
Deposited Residue Count: 288
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Caltubin, EF-hand	A, B	144	Lymnaea stagnalis	Mutation(s): 0
UniProt
Find proteins for Q2VA57 (Lymnaea stagnalis) Explore Q2VA57 Go to UniProtKB: Q2VA57
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2VA57
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SR Query on SR Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B]	STRONTIUM ION Sr PWYYWQHXAPXYMF-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain U [auth B] MOL2 format, chain K [auth A] MOL2 format, chain U [auth B]	K [auth A], U [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain U [auth B] Interactions & Density Focus chain K [auth A] Focus chain U [auth B]
UNX Query on UNX Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain V [auth B] SDF format, chain W [auth B] MOL2 format, chain L [auth A] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B]	L [auth A], V [auth B], W [auth B]	UNKNOWN ATOM OR ION X		Interactions Focus chain L [auth A] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain L [auth A] Focus chain V [auth B] Focus chain W [auth B]