8Y6B | pdb_00008y6b

Structure of human LGI1-ADAM22 complex in space group P212121

PDB DOI: https://doi.org/10.2210/pdb8Y6B/pdb

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

Deposited: 2024-02-02 Released: 2024-02-14
Deposition Author(s): Liu, H., Xu, F.
Funding Organization(s): National Science Foundation (NSF, China)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.49 Å
R-Value Free:
0.277 (Depositor), 0.273 (DCC)
R-Value Work:
0.236 (Depositor), 0.235 (DCC)
R-Value Observed:
0.238 (Depositor)

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structure of human LGI1-ADAM22 complex in space group P212121

Liu, H., Xu, F.

To be published.

Macromolecule Content

Total Structure Weight: 347.54 kDa
Atom Count: 24,226
Modeled Residue Count: 3,009
Deposited Residue Count: 3,036
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], D [auth C]	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] Focus chain D [auth C]	Go to GlyGen: Q9P0K1-1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Leucine-rich glioma-inactivated protein 1	B [auth D], E [auth F], F [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 E [auth F] Focus chain F [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 Y [auth C] SDF format, chain X [auth C] SDF format, chain W [auth C] SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain O [auth D] SDF format, chain N [auth D] SDF format, chain M [auth D] SDF format, chain IA [auth E] SDF format, chain I [auth A] SDF format, chain HA [auth E] SDF format, chain H [auth A] SDF format, chain GA [auth E] SDF format, chain G [auth A] SDF format, chain EA [auth F] SDF format, chain DA [auth F] SDF format, chain CA [auth F] MOL2 format, chain Y [auth C] MOL2 format, chain X [auth C] MOL2 format, chain W [auth C] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain O [auth D] MOL2 format, chain N [auth D] MOL2 format, chain M [auth D] MOL2 format, chain IA [auth E] MOL2 format, chain I [auth A] MOL2 format, chain HA [auth E] MOL2 format, chain H [auth A] MOL2 format, chain GA [auth E] MOL2 format, chain G [auth A] MOL2 format, chain EA [auth F] MOL2 format, chain DA [auth F] MOL2 format, chain CA [auth F] mmCIF format, chain Y [auth C] mmCIF format, chain X [auth C] mmCIF format, chain W [auth C] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain O [auth D] mmCIF format, chain N [auth D] mmCIF format, chain M [auth D] mmCIF format, chain IA [auth E] mmCIF format, chain I [auth A] mmCIF format, chain HA [auth E] mmCIF format, chain H [auth A] mmCIF format, chain GA [auth E] mmCIF format, chain G [auth A] mmCIF format, chain EA [auth F] mmCIF format, chain DA [auth F] mmCIF format, chain CA [auth F]	CA [auth F] DA [auth F] EA [auth F] G [auth A] GA [auth E] CA [auth F], DA [auth F], EA [auth F], G [auth A], GA [auth E], H [auth A], HA [auth E], I [auth A], IA [auth E], M [auth D], N [auth D], O [auth D], Q [auth B], R [auth B], S [auth B], W [auth C], X [auth C], Y [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain CA [auth F] Focus chain DA [auth F] Focus chain EA [auth F] Focus chain G [auth A] Focus chain GA [auth E] Focus chain H [auth A] Focus chain HA [auth E] Focus chain I [auth A] Focus chain IA [auth E] Focus chain M [auth D] Focus chain N [auth D] Focus chain O [auth D] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Interactions & Density Focus chain CA [auth F] Focus chain DA [auth F] Focus chain EA [auth F] Focus chain G [auth A] Focus chain GA [auth E] Focus chain H [auth A] Focus chain HA [auth E] Focus chain I [auth A] Focus chain IA [auth E] Focus chain M [auth D] Focus chain N [auth D] Focus chain O [auth D] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain Z [auth C] SDF format, chain V [auth B] SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain P [auth D] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain JA [auth E] SDF format, chain J [auth A] SDF format, chain FA [auth F] SDF format, chain BA [auth C] SDF format, chain AA [auth C] MOL2 format, chain Z [auth C] MOL2 format, chain V [auth B] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain P [auth D] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain JA [auth E] MOL2 format, chain J [auth A] MOL2 format, chain FA [auth F] MOL2 format, chain BA [auth C] MOL2 format, chain AA [auth C] mmCIF format, chain Z [auth C] mmCIF format, chain V [auth B] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain P [auth D] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain JA [auth E] mmCIF format, chain J [auth A] mmCIF format, chain FA [auth F] mmCIF format, chain BA [auth C] mmCIF format, chain AA [auth C]	AA [auth C] BA [auth C] FA [auth F] J [auth A] JA [auth E] AA [auth C], BA [auth C], FA [auth F], J [auth A], JA [auth E], K [auth A], L [auth A], P [auth D], T [auth B], U [auth B], V [auth B], Z [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain FA [auth F] Focus chain J [auth A] Focus chain JA [auth E] Focus chain K [auth A] Focus chain L [auth A] Focus chain P [auth D] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain FA [auth F] Focus chain J [auth A] Focus chain JA [auth E] Focus chain K [auth A] Focus chain L [auth A] Focus chain P [auth D] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain Z [auth C]