8E57

Rabbit L-type voltage-gated calcium channel Cav1.1 in the presence of Amiodarone and 100 microM MNI-1 at 2.8 Angstrom resolution

PDB DOI: https://doi.org/10.2210/pdb8E57/pdb
EM Map EMD-27905: EMDB EMDataResource

Classification: TRANSPORT PROTEIN
Organism(s): Oryctolagus cuniculus
Mutation(s): No
Membrane Protein: Yes OPMPDBTMmpstruc

Deposited: 2022-08-20 Released: 2022-12-07
Deposition Author(s): Gao, S., Yao, X., Yan, N.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.80 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Macromolecule Content

Total Structure Weight: 368.8 kDa
Atom Count: 18,449
Modelled Residue Count: 2,247
Deposited Residue Count: 3,201
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Voltage-dependent L-type calcium channel subunit alpha-1S	A	1,873	Oryctolagus cuniculus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P07293 (Oryctolagus cuniculus) Explore P07293 Go to UniProtKB: P07293
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P07293
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Voltage-dependent calcium channel gamma-1 subunit	B [auth E]	222	Oryctolagus cuniculus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P19518 (Oryctolagus cuniculus) Explore P19518 Go to UniProtKB: P19518
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P19518
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Voltage-dependent calcium channel subunit alpha-2/delta-1	C [auth F]	1,106	Oryctolagus cuniculus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P13806 (Oryctolagus cuniculus) Explore P13806 Go to UniProtKB: P13806
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P13806
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth B], E [auth C], F [auth D], G	2	N/A	N-Glycosylation	Interactions Focus chain D [auth B] Focus chain E [auth C] Focus chain F [auth D] Focus chain G Interactions & Density Focus chain D [auth B] Focus chain E [auth C] Focus chain F [auth D] Focus chain G
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H	3	N/A	N-Glycosylation	Interactions Focus chain H Interactions & Density Focus chain H
Glycosylation Resources
GlyTouCan: G47362BJ GlyCosmos: G47362BJ GlyGen: G47362BJ

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	I, J	3	N/A	N-Glycosylation	Interactions Focus chain I Focus chain J Interactions & Density Focus chain I Focus chain J
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BBI (Subject of Investigation/LOI) Query on BBI Download Ideal Coordinates CCD File SDF format, chain L [auth A] MOL2 format, chain L [auth A]	L [auth A]	(2-butyl-1-benzofuran-3-yl){4-[2-(diethylamino)ethoxy]-3,5-diiodophenyl}methanone C₂₅ H₂₉ I₂ N O₃ IYIKLHRQXLHMJQ-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Interactions & Density Focus chain L [auth A]
WFR (Subject of Investigation/LOI) Query on WFR Download Ideal Coordinates CCD File SDF format, chain M [auth A] MOL2 format, chain M [auth A]	M [auth A]	propan-2-yl (2S)-2-{[(S)-{[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-4-ethynyl-3-hydroxy-4-methyloxolan-2-yl]methoxy}(phenoxy)phosphoryl]amino}propanoate (non-preferred name) C₂₄ H₃₀ N₃ O₉ P HVOMZYITEDRMBB-XSZHHMMYSA-N		Interactions Focus chain M [auth A] Interactions & Density Focus chain M [auth A]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain O [auth F] SDF format, chain P [auth F] SDF format, chain Q [auth F] SDF format, chain R [auth F] SDF format, chain S [auth F] SDF format, chain T [auth F] SDF format, chain U [auth F] MOL2 format, chain O [auth F] MOL2 format, chain P [auth F] MOL2 format, chain Q [auth F] MOL2 format, chain R [auth F] MOL2 format, chain S [auth F] MOL2 format, chain T [auth F] MOL2 format, chain U [auth F]	O [auth F] P [auth F] Q [auth F] R [auth F] S [auth F] O [auth F], P [auth F], Q [auth F], R [auth F], S [auth F], T [auth F], U [auth F]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain O [auth F] Focus chain P [auth F] Focus chain Q [auth F] Focus chain R [auth F] Focus chain S [auth F] Focus chain T [auth F] Focus chain U [auth F] Interactions & Density Focus chain O [auth F] Focus chain P [auth F] Focus chain Q [auth F] Focus chain R [auth F] Focus chain S [auth F] Focus chain T [auth F] Focus chain U [auth F]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain N [auth F] MOL2 format, chain K [auth A] MOL2 format, chain N [auth F]	K [auth A], N [auth F]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain N [auth F] Interactions & Density Focus chain K [auth A] Focus chain N [auth F]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 5
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900017 Query on PRD_900017	H	triacetyl-beta-chitotriose	Oligosaccharide / Inhibitor		Interactions Focus chain H Interactions & Density Focus chain H