7YIZ | pdb_00007yiz

Crystal structure of anti-mPEG h15-2b Fab W104Y mutant

PDB DOI: https://doi.org/10.2210/pdb7YIZ/pdb

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

Deposited: 2022-07-18 Released: 2023-08-02
Deposition Author(s): Chang, C.Y., Nguyen, T.M.T., Li, Y.C., Su, Y.C.
Funding Organization(s): Ministry of Science and Technology (MoST, Taiwan)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.42 Å
R-Value Free:
0.270 (Depositor), 0.268 (DCC)
R-Value Work:
0.216 (Depositor), 0.217 (DCC)
R-Value Observed:
0.218 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Engineering a High-Affinity Anti-Methoxy Poly(ethylene glycol) (mPEG) Antibody for Sensitive Immunosensing of mPEGylated Therapeutics and mPEG Molecules

Hsiao, C.Y., Meng, J.L., Hong, J.Z., Ly, X.H., Lin, M.H., Chang, C.Y., Nguyen, M.T.T., Cheng, T.L., Lin, W.W., Burnouf, P.A., Al-Qaisi, T.S., Liu, E.S., Su, Y.C.

(2022) Bioconjug Chem 33: 2180-2188

DOI: https://doi.org/10.1021/acs.bioconjchem.2c00416

Macromolecule Content

Total Structure Weight: 96.82 kDa
Atom Count: 6,608
Modeled Residue Count: 845
Deposited Residue Count: 886
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
15-2b light chain	A, C	214	Homo sapiens	Mutation(s): 0

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
15-2b W104Y heavy chain	B, D	229	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
P15 (Subject of Investigation/LOI) Query on P15 Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain F [auth D] MOL2 format, chain E [auth B] MOL2 format, chain F [auth D] mmCIF format, chain E [auth B] mmCIF format, chain F [auth D]	E [auth B], F [auth D]	2,5,8,11,14,17-HEXAOXANONADECAN-19-OL C₁₃ H₂₈ O₇ FHHGCKHKTAJLOM-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Focus chain F [auth D] Interactions & Density Focus chain E [auth B] Focus chain F [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.42 Å
R-Value Free: 0.270 (Depositor), 0.268 (DCC)
R-Value Work: 0.216 (Depositor), 0.217 (DCC)
R-Value Observed: 0.218 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.335	α = 90
b = 112.056	β = 90
c = 157.792	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-08-02

Deposition Author(s):

Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, Taiwan)	Taiwan	MOST109-2636-B-009-003
Ministry of Science and Technology (MoST, Taiwan)	Taiwan	110-2113-M-A49-026-MY3

Revision History (Full details and data files)

Version 1.0: 2023-08-02
Type: Initial release
Version 1.1: 2024-10-23
Changes: Data collection, Structure summary
Version 1.2: 2025-02-12
Changes: Database references
Version 1.3: 2026-03-04
Changes: Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.