6JU0

Mouse antibody 3.3 Fab in complex with PEG

PDB DOI: https://doi.org/10.2210/pdb6JU0/pdb

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

Deposited: 2019-04-12 Released: 2020-02-05
Deposition Author(s): Lee, C.C., Ko, T.P., Lin, L.L., Wang, A.H.J.
Funding Organization(s): Academia Sinica (Taiwan)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.240
R-Value Work: 0.211
R-Value Observed: 0.212

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: 190.31 kDa
Atom Count: 14,026
Modelled Residue Count: 1,702
Deposited Residue Count: 1,728
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab heavy chain	A [auth H], C [auth I], E [auth J], G [auth K]	219	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
Fab light chain	B [auth L], D [auth M], F [auth N], H [auth O]	213	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
PE3 Query on PE3 Download Ideal Coordinates CCD File SDF format, chain K [auth I] SDF format, chain N [auth K] MOL2 format, chain K [auth I] MOL2 format, chain N [auth K]	K [auth I], N [auth K]	3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL C₂₈ H₅₈ O₁₅ ILLKMACMBHTSHP-UHFFFAOYSA-N		Interactions Focus chain K [auth I] Focus chain N [auth K] Interactions & Density Focus chain K [auth I] Focus chain N [auth K]
1PE Query on 1PE Download Ideal Coordinates CCD File SDF format, chain I [auth H] MOL2 format, chain I [auth H]	I [auth H]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain I [auth H] Interactions & Density Focus chain I [auth H]
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain P [auth K] MOL2 format, chain P [auth K]	P [auth K]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain P [auth K] Interactions & Density Focus chain P [auth K]
TOE Query on TOE Download Ideal Coordinates CCD File SDF format, chain J [auth H] SDF format, chain L [auth I] SDF format, chain M [auth J] SDF format, chain O [auth K] MOL2 format, chain J [auth H] MOL2 format, chain L [auth I] MOL2 format, chain M [auth J] MOL2 format, chain O [auth K]	J [auth H], L [auth I], M [auth J], O [auth K]	2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL C₇ H₁₆ O₄ JLGLQAWTXXGVEM-UHFFFAOYSA-N		Interactions Focus chain J [auth H] Focus chain L [auth I] Focus chain M [auth J] Focus chain O [auth K] Interactions & Density Focus chain J [auth H] Focus chain L [auth I] Focus chain M [auth J] Focus chain O [auth K]