6JWC

Mouse antibody 2B5 Fab in complex with PEG

PDB DOI: https://doi.org/10.2210/pdb6JWC/pdb

Classification: IMMUNE SYSTEM
Organism(s): Mus musculus
Expression System: Lentivirus
Mutation(s): No

Deposited: 2019-04-19 Released: 2020-02-05
Deposition Author(s): Lee, C.C., Ko, T.P., Su, Y.C., Lin, L.L., Roffler, S.R., Wang, A.H.J.
Funding Organization(s): Academia Sinica (Taiwan)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.226
R-Value Work: 0.187
R-Value Observed: 0.189

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structural basis of polyethylene glycol recognition by antibody.

Lee, C.C., Su, Y.C., Ko, T.P., Lin, L.L., Yang, C.Y., Chang, S.S., Roffler, S.R., Wang, A.H.

(2020) J Biomed Sci 27: 12-12

PubMed: 31907057 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1186/s12929-019-0589-7
Primary Citation of Related Structures:
6JP7, 6JU0, 6JWC

PubMed Abstract:
Polyethylene glycol (PEG) is widely used in industry and medicine. Anti-PEG antibodies have been developed for characterizing PEGylated drugs and other applications. However, the underlying mechanism for specific PEG binding has not been elucidated.

Organizational Affiliation

Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan. chengung@gate.sinica.edu.tw.

Macromolecule Content

Total Structure Weight: 49.9 kDa
Atom Count: 3,799
Modelled Residue Count: 425
Deposited Residue Count: 436
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Immunoglobulin heavy chain Fab fragment	A [auth H]	221	Mus musculus	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
Immunoglobulin light chain	B [auth L]	215	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
12P (Subject of Investigation/LOI) Query on 12P Download Ideal Coordinates CCD File SDF format, chain G [auth H] MOL2 format, chain G [auth H]	G [auth H]	DODECAETHYLENE GLYCOL C₂₄ H₅₀ O₁₃ WRZXKWFJEFFURH-UHFFFAOYSA-N		Interactions Focus chain G [auth H] Interactions & Density Focus chain G [auth H]
O4B Query on O4B Download Ideal Coordinates CCD File SDF format, chain H SDF format, chain I [auth H] SDF format, chain J [auth H] SDF format, chain M [auth L] SDF format, chain N [auth L] MOL2 format, chain H MOL2 format, chain I [auth H] MOL2 format, chain J [auth H] MOL2 format, chain M [auth L] MOL2 format, chain N [auth L]	H, I [auth H], J [auth H], M [auth L], N [auth L]	1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE C₁₂ H₂₄ O₆ XEZNGIUYQVAUSS-UHFFFAOYSA-N		Interactions Focus chain H Focus chain I [auth H] Focus chain J [auth H] Focus chain M [auth L] Focus chain N [auth L] Interactions & Density Focus chain H Focus chain I [auth H] Focus chain J [auth H] Focus chain M [auth L] Focus chain N [auth L]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain L MOL2 format, chain L	L	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain L Interactions & Density Focus chain L
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth H] SDF format, chain D [auth H] SDF format, chain E [auth H] SDF format, chain F [auth H] SDF format, chain K [auth L] MOL2 format, chain C [auth H] MOL2 format, chain D [auth H] MOL2 format, chain E [auth H] MOL2 format, chain F [auth H] MOL2 format, chain K [auth L]	C [auth H], D [auth H], E [auth H], F [auth H], K [auth L]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth H] Focus chain D [auth H] Focus chain E [auth H] Focus chain F [auth H] Focus chain K [auth L] Interactions & Density Focus chain C [auth H] Focus chain D [auth H] Focus chain E [auth H] Focus chain F [auth H] Focus chain K [auth L]