8SIP | pdb_00008sip

Structure of a mouse IgG antibody fragment that binds Inosine, an RNA modification

PDB DOI: https://doi.org/10.2210/pdb8SIP/pdb

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

Deposited: 2023-04-16 Released: 2024-02-07
Deposition Author(s): Aoki, S.T.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free:
0.245 (Depositor), 0.240 (DCC)
R-Value Work:
0.204 (Depositor), 0.200 (DCC)
R-Value Observed:
0.206 (Depositor)

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 fragment that binds Inosine, an RNA modification

Aoki, S.T.

To be published.

Macromolecule Content

Total Structure Weight: 48.51 kDa
Atom Count: 3,531
Modeled Residue Count: 426
Deposited Residue Count: 441
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inosine binding IgG Fab, heavy chain	A [auth H]	222	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
Inosine binding IgG Fab, kappa chain	B [auth L]	219	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NOS (Subject of Investigation/LOI) Query on NOS Download Ideal Coordinates CCD File SDF format, chain C [auth H] MOL2 format, chain C [auth H] mmCIF format, chain C [auth H]	C [auth H]	INOSINE C₁₀ H₁₂ N₄ O₅ UGQMRVRMYYASKQ-KQYNXXCUSA-N		Interactions Focus chain C [auth H] Interactions & Density Focus chain C [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free: 0.245 (Depositor), 0.240 (DCC)
R-Value Work: 0.204 (Depositor), 0.200 (DCC)
R-Value Observed: 0.206 (Depositor)

Diffraction Data: https://doi.org/10.18430/M38SIP

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.817	α = 83.84
b = 49.09	β = 88.82
c = 57.385	γ = 89.68

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data processing
Aimless	data scaling
PHASER	phasing
Coot	model building
autoPROC	data reduction

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-02-07

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2024-02-07
Type: Initial release
Version 1.1: 2024-11-06
Changes: Structure summary

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.