Macromolecule Content

Total Structure Weight: 49.91 kDa
Atom Count: 4091
Residue Count: 451
Unique protein chains: 3

6UOE

3-25 Fab germline-reversion variant bound to an HCMV gB-derived peptide

DOI: 10.2210/pdb6UOE/pdb

Classification: IMMUNE SYSTEM/VIRAL PROTEIN
Organism(s): Homo sapiens, Human betaherpesvirus 5
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2019-10-14 Released: 2020-07-29
Deposition Author(s): Wrapp, D., McLellan, J.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.186
R-Value Work: 0.160
R-Value Observed: 0.162

wwPDB Validation 3D Report Full Report

Literature

Characterization of a broadly neutralizing antibody that recognizes antigenic domain-2 of HCMV gB

Ye, X., Su, H., Wrapp, D., Freed, D.C., Li, F., Yuan, Z., Tang, A., Li, L., Ku, Z., Xiong, W., Liu, J., Zhu, H., Ma, N., Wang, D., McLellan, J.S., Zhang, N., Fu, T.M., An, Z.

To be published.

Macromolecules

Find similar proteins by:

(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-25 Fab heavy chain	H	229	Homo sapiens	Mutation(s): 0
Find proteins for P0DOX5 (Homo sapiens) Explore P0DOX5 Go to UniProtKB: P0DOX5
Protein Feature View Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
3-25 Fab light chain	L	215	Homo sapiens	Mutation(s): 0
Find proteins for P0DOX7 (Homo sapiens) Explore P0DOX7 Go to UniProtKB: P0DOX7
Protein Feature View Expand
Reference Sequence

Find similar proteins by: Sequence | Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein B	P	15	Human betaherpesvirus 5	Mutation(s): 0
Find proteins for P06473 (Human cytomegalovirus (strain AD169)) Explore P06473 Go to UniProtKB: P06473
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain D [L] MOL2 format, chain D [L]	L	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Ligand Interaction
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain E [L] MOL2 format, chain E [L]	L	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Ligand Interaction

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA Query on PCA	H	L-PEPTIDE LINKING	C₅ H₇ N O₃		GLN

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.186
R-Value Work: 0.160
R-Value Observed: 0.162
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.663	α = 90
b = 67.587	β = 133.12
c = 84.031	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Deposited Date: 2019-10-14
Released Date: 2020-07-29

Deposition Author(s):

Revision History

Version 1.0: 2020-07-29
Type: Initial release

RCSB PDB is funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.