8T51

Crystal structure of Fab 3.10C2 bound to TREM2

PDB DOI: https://doi.org/10.2210/pdb8T51/pdb

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

Deposited: 2023-06-12 Released: 2024-06-19
Deposition Author(s): Hsu, P.L., Wallweber, H.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.240
R-Value Work: 0.193

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.A., 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: 102.73 kDa
Atom Count: 7,605
Modelled Residue Count: 894
Deposited Residue Count: 922
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3.10C2 Fab heavy chain	A, C	222	Homo sapiens	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
3.10C2 Fab light chain	B, D	219	Homo sapiens	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 peptide	E, F	20	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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain JA [auth E] SDF format, chain NA [auth F] SDF format, chain T [auth B] SDF format, chain U [auth B] MOL2 format, chain JA [auth E] MOL2 format, chain NA [auth F] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B]	JA [auth E], NA [auth F], T [auth B], U [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain JA [auth E] Focus chain NA [auth F] Focus chain T [auth B] Focus chain U [auth B] Interactions & Density Focus chain JA [auth E] Focus chain NA [auth F] Focus chain T [auth B] Focus chain U [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain DA [auth D] SDF format, chain EA [auth D] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain Z [auth C] MOL2 format, chain DA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain Z [auth C]	DA [auth D] EA [auth D] G [auth A] H [auth A] I [auth A] DA [auth D], EA [auth D], G [auth A], H [auth A], I [auth A], P [auth B], Q [auth B], Z [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain DA [auth D] Focus chain EA [auth D] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain Z [auth C] Interactions & Density Focus chain DA [auth D] Focus chain EA [auth D] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain Z [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BA [auth C] SDF format, chain FA [auth D] SDF format, chain GA [auth D] SDF format, chain IA [auth D] SDF format, chain K [auth A] SDF format, chain N [auth A] SDF format, chain R [auth B] SDF format, chain S [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain FA [auth D] MOL2 format, chain GA [auth D] MOL2 format, chain IA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain N [auth A] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B]	AA [auth C] BA [auth C] FA [auth D] GA [auth D] IA [auth D] AA [auth C], BA [auth C], FA [auth D], GA [auth D], IA [auth D], K [auth A], N [auth A], R [auth B], S [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain IA [auth D] Focus chain K [auth A] Focus chain N [auth A] Focus chain R [auth B] Focus chain S [auth B] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain IA [auth D] Focus chain K [auth A] Focus chain N [auth A] Focus chain R [auth B] Focus chain S [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain KA [auth E] SDF format, chain LA [auth F] SDF format, chain M [auth A] SDF format, chain MA [auth F] SDF format, chain O [auth A] SDF format, chain V [auth B] SDF format, chain Y [auth B] MOL2 format, chain J [auth A] MOL2 format, chain KA [auth E] MOL2 format, chain LA [auth F] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth F] MOL2 format, chain O [auth A] MOL2 format, chain V [auth B] MOL2 format, chain Y [auth B]	J [auth A] KA [auth E] LA [auth F] M [auth A] MA [auth F] J [auth A], KA [auth E], LA [auth F], M [auth A], MA [auth F], O [auth A], V [auth B], Y [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain KA [auth E] Focus chain LA [auth F] Focus chain M [auth A] Focus chain MA [auth F] Focus chain O [auth A] Focus chain V [auth B] Focus chain Y [auth B] Interactions & Density Focus chain J [auth A] Focus chain KA [auth E] Focus chain LA [auth F] Focus chain M [auth A] Focus chain MA [auth F] Focus chain O [auth A] Focus chain V [auth B] Focus chain Y [auth B]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain HA [auth D] SDF format, chain L [auth A] SDF format, chain W [auth B] SDF format, chain X [auth B] MOL2 format, chain CA [auth C] MOL2 format, chain HA [auth D] MOL2 format, chain L [auth A] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B]	CA [auth C], HA [auth D], L [auth A], W [auth B], X [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain CA [auth C] Focus chain HA [auth D] Focus chain L [auth A] Focus chain W [auth B] Focus chain X [auth B] Interactions & Density Focus chain CA [auth C] Focus chain HA [auth D] Focus chain L [auth A] Focus chain W [auth B] Focus chain X [auth B]