46GH | pdb_000046gh

Crystal structure of a de novo-designed VHH targeting BHRF1

PDB DOI: https://doi.org/10.2210/pdb46GH/pdb

Classification: DE NOVO PROTEIN
Organism(s): Epstein-barr virus strain ag876, synthetic construct
Expression System: Escherichia coli, Cricetulus griseus
Mutation(s): No

Deposited: 2026-09-21 Released: 2026-10-28
Deposition Author(s): Wang, S., Yu, Q.L., Tian, B.H., Qin, X.Y., Chen, M.C.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.40 Å
R-Value Free:
0.251 (Depositor), 0.258 (DCC)
R-Value Work:
0.204 (Depositor), 0.210 (DCC)
R-Value Observed:
0.207 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Validation slider image for 46GH

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

Literature

High-Affinity Protein Binder Design via Flow Matching and In Silico Maturation

Yu, Q.L., Guo, L.Y., Qin, X.Y., Huang, X.K., Tian, B.H., Wang, H.Z., Liu, Y., Wang, S., Lang, Y.Z., Shen, Z.H.Y., Lin, J., Chen, M.C.

To be published.

Macromolecule Content

Total Structure Weight: 327.1 kDa
Atom Count: 22,139
Modeled Residue Count: 2,810
Deposited Residue Count: 2,920
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Apoptosis regulator BHRF1	A, C, E, G, I A, C, E, G, I, K, M, O, Q, S	160	Epstein-barr virus strain ag876	Mutation(s): 0 Gene Names: BHRF1
UniProt
Find proteins for P0C6Z1 (Epstein-Barr virus (strain AG876)) Explore P0C6Z1 Go to UniProtKB: P0C6Z1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0C6Z1
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
BHRF1_VHH-N13	B, D, F, H, J B, D, F, H, J, L, N, P, R, T	132	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.40 Å
R-Value Free: 0.251 (Depositor), 0.258 (DCC)
R-Value Work: 0.204 (Depositor), 0.210 (DCC)
R-Value Observed: 0.207 (Depositor)

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.638	α = 90
b = 196.378	β = 90
c = 214.597	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-10-28

Deposition Author(s):

Funding Organization	Location	Grant Number
Other government	China	--

Revision History (Full details and data files)

Version 1.0: 2026-10-28
Type: Initial release