8VEV

Structure of a mouse IgG antibody antigen-binding fragment (Fab) targeting N6-methyladenosine (m6A), an RNA modification, m6A nucleoside ligand

PDB DOI: https://doi.org/10.2210/pdb8VEV/pdb

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

Deposited: 2023-12-20 Released: 2024-02-07
Deposition Author(s): Aoki, S.T.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.06 Å
R-Value Free: 0.253
R-Value Work: 0.224
R-Value Observed: 0.225

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structure of a mouse IgG antibody antigen-binding fragment (Fab) targeting N6-methyladenosine (m6A), an RNA modification, m6A nucleoside ligand

Aoki, S.T.

To be published.

Macromolecule Content

Total Structure Weight: 143.05 kDa
Atom Count: 9,801
Modelled Residue Count: 1,267
Deposited Residue Count: 1,308
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N6-methyladenosine (m6A) binding IgG Fab, heavy chain	A, C, E [auth H]	221	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
N6-methyladenosine (m6A) binding IgG Fab, light chain	B, D, F [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
6MD (Subject of Investigation/LOI) Query on 6MD Download Ideal Coordinates CCD File SDF format, chain J [auth C] SDF format, chain R [auth H] MOL2 format, chain J [auth C] MOL2 format, chain R [auth H] mmCIF format, chain J [auth C] mmCIF format, chain R [auth H]	J [auth C], R [auth H]	N-methyladenosine C₁₁ H₁₅ N₅ O₄ VQAYFKKCNSOZKM-IOSLPCCCSA-N		Interactions Focus chain J [auth C] Focus chain R [auth H] Interactions & Density Focus chain J [auth C] Focus chain R [auth H]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain K [auth C] SDF format, chain L [auth D] SDF format, chain M [auth D] SDF format, chain N [auth D] SDF format, chain O [auth H] SDF format, chain P [auth H] SDF format, chain Q [auth H] SDF format, chain T [auth L] SDF format, chain U [auth L] SDF format, chain V [auth L] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain K [auth C] MOL2 format, chain L [auth D] MOL2 format, chain M [auth D] MOL2 format, chain N [auth D] MOL2 format, chain O [auth H] MOL2 format, chain P [auth H] MOL2 format, chain Q [auth H] MOL2 format, chain T [auth L] MOL2 format, chain U [auth L] MOL2 format, chain V [auth L] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain K [auth C] mmCIF format, chain L [auth D] mmCIF format, chain M [auth D] mmCIF format, chain N [auth D] mmCIF format, chain O [auth H] mmCIF format, chain P [auth H] mmCIF format, chain Q [auth H] mmCIF format, chain T [auth L] mmCIF format, chain U [auth L] mmCIF format, chain V [auth L]	H [auth B] I [auth B] K [auth C] L [auth D] M [auth D] H [auth B], I [auth B], K [auth C], L [auth D], M [auth D], N [auth D], O [auth H], P [auth H], Q [auth H], T [auth L], U [auth L], V [auth L]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain H [auth B] Focus chain I [auth B] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth D] Focus chain N [auth D] Focus chain O [auth H] Focus chain P [auth H] Focus chain Q [auth H] Focus chain T [auth L] Focus chain U [auth L] Focus chain V [auth L] Interactions & Density Focus chain H [auth B] Focus chain I [auth B] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth D] Focus chain N [auth D] Focus chain O [auth H] Focus chain P [auth H] Focus chain Q [auth H] Focus chain T [auth L] Focus chain U [auth L] Focus chain V [auth L]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain S [auth H] MOL2 format, chain S [auth H] mmCIF format, chain S [auth H]	S [auth H]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain S [auth H] Interactions & Density Focus chain S [auth H]