5Y2K

A human antibody AF4H1L1

PDB DOI: https://doi.org/10.2210/pdb5Y2K/pdb

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

Deposited: 2017-07-26 Released: 2019-01-30
Deposition Author(s): Xiao, H., Qi, J., Gao, F.G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.259
R-Value Work: 0.220

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

An H3-clade neutralizing antibody screened from an H7N9 patient that binds group 2 influenza A hemagglutinins

Xiao, H., Qi, J., Gao, F.G.

To be published.

Macromolecule Content

Total Structure Weight: 193.58 kDa
Atom Count: 13,469
Modelled Residue Count: 1,714
Deposited Residue Count: 1,804
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
a group 2 HA binding antibody AF4H1K1 Fab heavy chain	A, C, E, G	233	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:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
a group 2 HA binding antibody AF4H1K1 Fab light chain	B, D, F, H	218	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.259
R-Value Work: 0.220
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.266	α = 90
b = 90.119	β = 102.38
c = 111.404	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2019-01-30

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2019-01-30
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description

RCSB PDB Core Operations are 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.