6H3H

Fab fragment of antibody against fullerene C60

PDB DOI: https://doi.org/10.2210/pdb6H3H/pdb

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

Deposited: 2018-07-18 Released: 2019-05-15
Deposition Author(s): Osipov, E.M., Tikhonova, T.V.
Funding Organization(s): Russian Science Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.92 Å
R-Value Free: 0.234
R-Value Work: 0.188
R-Value Observed: 0.191

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Structure of the Anti-C60 Fullerene Antibody Fab Fragment: Structural Determinants of Fullerene Binding.

Osipov, E.M., Hendrickson, O.D., Tikhonova, T.V., Zherdev, A.V., Solopova, O.N., Sveshnikov, P.G., Dzantiev, B.B., Popov, V.O.

(2019) Acta Naturae 11: 58-65

PubMed: 31024749 Search on PubMedSearch on PubMed Central
Primary Citation of Related Structures:
6H3H

PubMed Abstract:
The structure of the anti-C ₆₀ fullerene antibody Fab fragment (FabC ₆₀) was solved by X-ray crystallography. The computer-aided docking of C ₆₀ into the antigen-binding pocket of FabC ₆₀ showed that binding of C ₆₀ to FabC ₆₀ is governed by the enthalpy and entropy; namely, by π-π stacking interactions with aromatic residues of the antigen-binding site and reduction of the solvent-accessible area of the hydrophobic surface of C ₆₀. A fragment of the mobile CDR H3 loop located on the surface of FabC ₆₀ interferes with C ₆₀ binding in the antigen-binding site, thereby resulting in low antibody affinity for C ₆₀. The structure of apo-FabC ₆₀ has been deposited with pdbid 6H3H.

Organizational Affiliation

Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, 119071, Moscow, Russia.

Macromolecule Content

Total Structure Weight: 94.75 kDa
Atom Count: 7,045
Modelled Residue Count: 866
Deposited Residue Count: 874
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Anti-fullerene antibody Fab fragment Heavy chain	A, C	222	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
Anti-fullerene antibody Fab fragment Light chain	B, D	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain I [auth C] SDF format, chain L [auth D] SDF format, chain M [auth D] SDF format, chain N [auth D] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain I [auth C] MOL2 format, chain L [auth D] MOL2 format, chain M [auth D] MOL2 format, chain N [auth D] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain I [auth C] mmCIF format, chain L [auth D] mmCIF format, chain M [auth D] mmCIF format, chain N [auth D]	G [auth B] H [auth B] I [auth C] L [auth D] M [auth D] G [auth B], H [auth B], I [auth C], L [auth D], M [auth D], N [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth C] Focus chain L [auth D] Focus chain M [auth D] Focus chain N [auth D] Interactions & Density Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth C] Focus chain L [auth D] Focus chain M [auth D] Focus chain N [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain J [auth D] SDF format, chain K [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain J [auth D] MOL2 format, chain K [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain J [auth D] mmCIF format, chain K [auth D]	E [auth A], F [auth B], J [auth D], K [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain J [auth D] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain J [auth D] Focus chain K [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.92 Å
R-Value Free: 0.234
R-Value Work: 0.188
R-Value Observed: 0.191
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.33	α = 90
b = 138.18	β = 91.85
c = 83.53	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
BALBES	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2019-05-15

Deposition Author(s):

Osipov, E.M.

Tikhonova, T.V.

Funding Organization	Location	Grant Number
Russian Science Foundation	Russian Federation	14-24-00172

Revision History (Full details and data files)

Version 1.0: 2019-05-15
Type: Initial release
Version 1.1: 2024-01-17
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-11-06
Changes: Structure summary