8T59

Crystal structure of Para.09 bound to TREM2

PDB DOI: https://doi.org/10.2210/pdb8T59/pdb

Classification: IMMUNE SYSTEM/PEPTIDE BINDING PROTEIN
Organism(s): synthetic construct, Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2023-06-12 Released: 2024-07-31
Deposition Author(s): Wallweber, H., Hsu, P.L.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.237
R-Value Work: 0.200
R-Value Observed: 0.202

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Rapid affinity optimization of an anti-TREM2 clinical lead antibody by cross-lineage immune repertoire mining

Hsiao, Y., Lin, Z., Du, C., Echeverria, A., Wallweber, H., Aung, T., Alberstein, R.G., Shang, Y., Seeger, F., Watkins, A., Seshasayee, D., Hansen, D.V., Bolen, C., Hsu, P.L., Hotzel, I.

To be published.

Macromolecule Content

Total Structure Weight: 101.86 kDa
Atom Count: 7,534
Modelled Residue Count: 895
Deposited Residue Count: 926
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Para.09 heavy chain	A, C	225	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Para.09 light chain	B, D	219	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Triggering receptor expressed on myeloid cells 2	E, F	19	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NZC2 (Homo sapiens) Explore Q9NZC2 Go to UniProtKB: Q9NZC2
PHAROS: Q9NZC2 GTEx: ENSG00000095970
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9NZC2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain S [auth C] MOL2 format, chain S [auth C]	S [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain S [auth C] Interactions & Density Focus chain S [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain T [auth D] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain T [auth D]	G [auth A] H [auth A] I [auth B] J [auth B] M [auth B] G [auth A], H [auth A], I [auth B], J [auth B], M [auth B], N [auth B], P [auth C], Q [auth C], R [auth C], T [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain T [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain T [auth D]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain O [auth B] SDF format, chain U [auth D] SDF format, chain V [auth D] SDF format, chain W [auth E] SDF format, chain X [auth F] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain O [auth B] MOL2 format, chain U [auth D] MOL2 format, chain V [auth D] MOL2 format, chain W [auth E] MOL2 format, chain X [auth F]	K [auth B] L [auth B] O [auth B] U [auth D] V [auth D] K [auth B], L [auth B], O [auth B], U [auth D], V [auth D], W [auth E], X [auth F]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Focus chain L [auth B] Focus chain O [auth B] Focus chain U [auth D] Focus chain V [auth D] Focus chain W [auth E] Focus chain X [auth F] Interactions & Density Focus chain K [auth B] Focus chain L [auth B] Focus chain O [auth B] Focus chain U [auth D] Focus chain V [auth D] Focus chain W [auth E] Focus chain X [auth F]