8TRV

Structure of the EphA2 LBDCRD bound to FabS1C_C1

PDB DOI: https://doi.org/10.2210/pdb8TRV/pdb

Classification: SIGNALING PROTEIN/IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2023-08-10 Released: 2024-07-17
Deposition Author(s): Singer, A.U., Bruce, H.A., Blazer, L., Adams, J.J., Sicheri, F., Sidhu, S.S.
Funding Organization(s): Celgene Corporation, Bristol-Myers Squibb (BMS) Research

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.25 Å
R-Value Free: 0.272
R-Value Work: 0.217
R-Value Observed: 0.220

Starting Models: 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

Synthetic Antibodies targeting EPHA2 Induce Diverse Signaling-Competent Clusters with Differential Activation

Adams, J.J., Bruce, H.A., Ploder, L., Garcia, J., Khutoreskaya, G., Jarvik, N., Costa, L.E., Gorelik, M., Pot, I., Sicheri, F., Blazer, L.L., Singer, A.U., Sidhu, S.S.

To be published.

Macromolecule Content

Total Structure Weight: 163.54 kDa
Atom Count: 10,692
Modelled Residue Count: 1,442
Deposited Residue Count: 1,492
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ephrin type-A receptor 2	A, F [auth B]	308	Homo sapiens	Mutation(s): 0 Gene Names: EPHA2, ECK EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P29317 (Homo sapiens) Explore P29317 Go to UniProtKB: P29317
PHAROS: P29317 GTEx: ENSG00000142627
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P29317
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
S1C variant of Fab_C1 heavy chain	B [auth C], D	223	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: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
S1C variant of Fab_C1 light chain	C [auth G], E	215	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IOD (Subject of Investigation/LOI) Query on IOD Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain N [auth G] SDF format, chain Q [auth D] SDF format, chain S [auth E] SDF format, chain W [auth B] MOL2 format, chain G [auth A] MOL2 format, chain N [auth G] MOL2 format, chain Q [auth D] MOL2 format, chain S [auth E] MOL2 format, chain W [auth B] mmCIF format, chain G [auth A] mmCIF format, chain N [auth G] mmCIF format, chain Q [auth D] mmCIF format, chain S [auth E] mmCIF format, chain W [auth B]	G [auth A], N [auth G], Q [auth D], S [auth E], W [auth B]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain N [auth G] Focus chain Q [auth D] Focus chain S [auth E] Focus chain W [auth B] Interactions & Density Focus chain G [auth A] Focus chain N [auth G] Focus chain Q [auth D] Focus chain S [auth E] Focus chain W [auth B]
EDO (Subject of Investigation/LOI) Query on EDO Download Ideal Coordinates CCD File SDF format, chain P [auth D] MOL2 format, chain P [auth D] mmCIF format, chain P [auth D]	P [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain P [auth D] Interactions & Density Focus chain P [auth D]
CL (Subject of Investigation/LOI) Query on CL Download Ideal Coordinates CCD File SDF format, chain X [auth B] SDF format, chain H [auth A] SDF format, chain K [auth C] SDF format, chain L [auth C] SDF format, chain O [auth G] SDF format, chain T [auth E] SDF format, chain U [auth E] SDF format, chain V [auth E] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain X [auth B] MOL2 format, chain H [auth A] MOL2 format, chain K [auth C] MOL2 format, chain L [auth C] MOL2 format, chain O [auth G] MOL2 format, chain T [auth E] MOL2 format, chain U [auth E] MOL2 format, chain V [auth E] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] mmCIF format, chain X [auth B] mmCIF format, chain H [auth A] mmCIF format, chain K [auth C] mmCIF format, chain L [auth C] mmCIF format, chain O [auth G] mmCIF format, chain T [auth E] mmCIF format, chain U [auth E] mmCIF format, chain V [auth E] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B]	H [auth A] K [auth C] L [auth C] O [auth G] T [auth E] H [auth A], K [auth C], L [auth C], O [auth G], T [auth E], U [auth E], V [auth E], X [auth B], Y [auth B], Z [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain K [auth C] Focus chain L [auth C] Focus chain O [auth G] Focus chain T [auth E] Focus chain U [auth E] Focus chain V [auth E] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain H [auth A] Focus chain K [auth C] Focus chain L [auth C] Focus chain O [auth G] Focus chain T [auth E] Focus chain U [auth E] Focus chain V [auth E] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
NA (Subject of Investigation/LOI) Query on NA Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain M [auth C] SDF format, chain R [auth D] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain M [auth C] MOL2 format, chain R [auth D] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain M [auth C] mmCIF format, chain R [auth D]	I [auth A], J [auth A], M [auth C], R [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth C] Focus chain R [auth D] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth C] Focus chain R [auth D]