8HPY | pdb_00008hpy

Crystal structure of human LGI1-ADAM22 complex

PDB DOI: https://doi.org/10.2210/pdb8HPY/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2022-12-13 Released: 2023-12-13
Deposition Author(s): Liu, H., Xu, F.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 5.87 Å
R-Value Free:
0.343 (Depositor), 0.336 (DCC)
R-Value Work:
0.303 (Depositor), 0.304 (DCC)
R-Value Observed:
0.305 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of human LGI1-ADAM22 complex

Liu, H., Xu, F.

To be published.

Macromolecule Content

Total Structure Weight: 231.69 kDa
Atom Count: 15,962
Modeled Residue Count: 1,998
Deposited Residue Count: 2,024
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Disintegrin and metalloproteinase domain-containing protein 22	A, C [auth B]	486	Homo sapiens	Mutation(s): 0 Gene Names: ADAM22, MDC2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9P0K1 (Homo sapiens) Explore Q9P0K1 Go to UniProtKB: Q9P0K1
PHAROS: Q9P0K1 GTEx: ENSG00000008277
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9P0K1
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain A Focus chain C [auth B]	Go to GlyGen: Q9P0K1-1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Leucine-rich glioma-inactivated protein 1	B [auth D], D [auth E]	526	Homo sapiens	Mutation(s): 0 Gene Names: LGI1, EPT, UNQ775/PRO1569
UniProt & NIH Common Fund Data Resources
Find proteins for O95970 (Homo sapiens) Explore O95970 Go to UniProtKB: O95970
PHAROS: O95970 GTEx: ENSG00000108231
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O95970
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain B [auth D] Focus chain D [auth E]	Go to GlyGen: O95970-1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain K [auth D] SDF format, chain M [auth D] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain U [auth E] SDF format, chain W [auth E] SDF format, chain V [auth E] SDF format, chain O [auth B] SDF format, chain L [auth D] SDF format, chain G [auth A] SDF format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain K [auth D] MOL2 format, chain M [auth D] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain U [auth E] MOL2 format, chain W [auth E] MOL2 format, chain V [auth E] MOL2 format, chain O [auth B] MOL2 format, chain L [auth D] MOL2 format, chain G [auth A] MOL2 format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain K [auth D] mmCIF format, chain M [auth D] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain U [auth E] mmCIF format, chain W [auth E] mmCIF format, chain V [auth E] mmCIF format, chain O [auth B] mmCIF format, chain L [auth D] mmCIF format, chain G [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] G [auth A] K [auth D] L [auth D] E [auth A], F [auth A], G [auth A], K [auth D], L [auth D], M [auth D], O [auth B], P [auth B], Q [auth B], U [auth E], V [auth E], W [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth D] Focus chain L [auth D] Focus chain M [auth D] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain U [auth E] Focus chain V [auth E] Focus chain W [auth E] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth D] Focus chain L [auth D] Focus chain M [auth D] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain U [auth E] Focus chain V [auth E] Focus chain W [auth E]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain R [auth B] SDF format, chain T [auth B] SDF format, chain X [auth E] SDF format, chain S [auth B] SDF format, chain N [auth D] SDF format, chain J [auth A] SDF format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain R [auth B] MOL2 format, chain T [auth B] MOL2 format, chain X [auth E] MOL2 format, chain S [auth B] MOL2 format, chain N [auth D] MOL2 format, chain J [auth A] MOL2 format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain R [auth B] mmCIF format, chain T [auth B] mmCIF format, chain X [auth E] mmCIF format, chain S [auth B] mmCIF format, chain N [auth D] mmCIF format, chain J [auth A] mmCIF format, chain H [auth A]	H [auth A] I [auth A] J [auth A] N [auth D] R [auth B] H [auth A], I [auth A], J [auth A], N [auth D], R [auth B], S [auth B], T [auth B], X [auth E]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain N [auth D] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain X [auth E] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain N [auth D] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain X [auth E]