7CZE

Crystal structure of Epstein-Barr virus (EBV) gHgL and in complex with the ligand binding domian (LBD) of EphA2

PDB DOI: https://doi.org/10.2210/pdb7CZE/pdb

Classification: VIRAL PROTEIN
Organism(s): Human herpesvirus 4 strain B95-8, Homo sapiens
Expression System: Trichoplusia ni, Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2020-09-08 Released: 2020-10-21
Deposition Author(s): Su, C., Wu, L.L., Song, H., Chai, Y., Qi, J.X., Yan, J.H., Gao, G.F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.285
R-Value Work: 0.257
R-Value Observed: 0.259

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.6 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 431.84 kDa
Atom Count: 29,320
Modelled Residue Count: 3,716
Deposited Residue Count: 3,836
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein H	A, C, E, G	662	Human herpesvirus 4 strain B95-8	Mutation(s): 0 Gene Names: gH, BXLF2
UniProt
Find proteins for P03231 (Epstein-Barr virus (strain B95-8)) Explore P03231 Go to UniProtKB: P03231
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P03231
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein L	B, D, F, H	114	Human herpesvirus 4 strain B95-8	Mutation(s): 0 Gene Names: gL, BKRF2
UniProt
Find proteins for P03212 (Epstein-Barr virus (strain B95-8)) Explore P03212 Go to UniProtKB: P03212
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P03212
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Ephrin type-A receptor 2	I, J, K, L	183	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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG (Subject of Investigation/LOI) Query on NAG Download Ideal Coordinates CCD File SDF format, chain AA [auth H] SDF format, chain BA [auth H] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain S [auth D] SDF format, chain T [auth D] SDF format, chain U [auth E] SDF format, chain V [auth E] SDF format, chain W [auth F] SDF format, chain X [auth F] SDF format, chain Y [auth G] SDF format, chain Z [auth G] MOL2 format, chain AA [auth H] MOL2 format, chain BA [auth H] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain S [auth D] MOL2 format, chain T [auth D] MOL2 format, chain U [auth E] MOL2 format, chain V [auth E] MOL2 format, chain W [auth F] MOL2 format, chain X [auth F] MOL2 format, chain Y [auth G] MOL2 format, chain Z [auth G]	AA [auth H] BA [auth H] M [auth A] N [auth A] O [auth B] AA [auth H], BA [auth H], M [auth A], N [auth A], O [auth B], P [auth B], Q [auth C], R [auth C], S [auth D], T [auth D], U [auth E], V [auth E], W [auth F], X [auth F], Y [auth G], Z [auth G]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth H] Focus chain BA [auth H] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth E] Focus chain V [auth E] Focus chain W [auth F] Focus chain X [auth F] Focus chain Y [auth G] Focus chain Z [auth G] Interactions & Density Focus chain AA [auth H] Focus chain BA [auth H] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth E] Focus chain V [auth E] Focus chain W [auth F] Focus chain X [auth F] Focus chain Y [auth G] Focus chain Z [auth G]