6KZP

calcium channel-ligand

PDB DOI: https://doi.org/10.2210/pdb6KZP/pdb
EM Map EMD-0792: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No
Membrane Protein: Yes OPMPDBTMMemProtMDmpstruc

Deposited: 2019-09-25 Released: 2019-12-18
Deposition Author(s): Yan, N.
Funding Organization(s): National Natural Science Foundation of China, Ministry of Science and Technology (China)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Macromolecule Content

Total Structure Weight: 247.67 kDa
Atom Count: 8,557
Modelled Residue Count: 1,014
Deposited Residue Count: 2,146
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Voltage-dependent T-type calcium channel subunit alpha-1G,Voltage-dependent T-type calcium channel subunit alpha-1G	A	2,146	Homo sapiens	Mutation(s): 0 Gene Names: CACNA1G, KIAA1123 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for O43497 (Homo sapiens) Explore O43497 Go to UniProtKB: O43497
PHAROS: O43497 GTEx: ENSG00000006283
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O43497
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
3PE Query on 3PE Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain L [auth A] SDF format, chain P [auth A] MOL2 format, chain K [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain L [auth A] MOL2 format, chain P [auth A]	I [auth A] J [auth A] K [auth A] L [auth A] M [auth A] I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A]	1,2-Distearoyl-sn-glycerophosphoethanolamine C₄₁ H₈₂ N O₈ P LVNGJLRDBYCPGB-LDLOPFEMSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A]
Y01 Query on Y01 Download Ideal Coordinates CCD File SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A]	Q [auth A], R [auth A], S [auth A]	CHOLESTEROL HEMISUCCINATE C₃₁ H₅₀ O₄ WLNARFZDISHUGS-MIXBDBMTSA-N		Interactions Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Interactions & Density Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A]
DZR (Subject of Investigation/LOI) Query on DZR Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A]	H [auth A]	~{N}-[[1-[2-(~{tert}-butylamino)-2-oxidanylidene-ethyl]piperidin-4-yl]methyl]-3-chloranyl-5-fluoranyl-benzamide C₁₉ H₂₇ Cl F N₃ O₂ JOCLITFYIMJMNK-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
NAG Query on NAG 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 G [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]	D [auth A], E [auth A], F [auth A], G [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A]	B [auth A], C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
DZR	BindingDB: 6KZP	IC50: 37 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2019-12-18

Deposition Author(s):

Yan, N.

Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	31621092
National Natural Science Foundation of China	China	31800628
National Natural Science Foundation of China	China	81920108015
Ministry of Science and Technology (China)	China	2016YFA0500402
Ministry of Science and Technology (China)	China	2016YFA0501100

Revision History (Full details and data files)

Version 1.0: 2019-12-18
Type: Initial release
Version 1.1: 2020-01-01
Changes: Database references
Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary

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Deposit Data

Help and Resources

6KZP

calcium channel-ligand

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)