9N7O | pdb_00009n7o

Designed anti-OSM Fab

PDB DOI: https://doi.org/10.2210/pdb9N7O/pdb

Classification: IMMUNE SYSTEM
Organism(s): Rattus norvegicus
Expression System: Cricetulus griseus
Mutation(s): No

Deposited: 2025-02-06 Released: 2026-02-11
Deposition Author(s): Kiefer, J.R., Alberstein, R.G., Hofmann, J.L., Watkins, A.M., Seeger, F., Dou, Y., Zhang, X.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.48 Å
R-Value Free:
0.205 (Depositor), 0.204 (DCC)
R-Value Work:
0.172 (Depositor), 0.171 (DCC)
R-Value Observed:
0.173 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Lab-in-the-loop therapeutic antibody design with deep learning

Frey, N.C., Hofmann, J.L., Kiefer, J.R., Alberstein, R.G., Seeger, F., Watkins, A.M., Bonneau, R.

To be published.

Macromolecule Content

Total Structure Weight: 48.17 kDa
Atom Count: 4,153
Modeled Residue Count: 442
Deposited Residue Count: 442
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
designed Fab heavy chain	A [auth H]	227	Rattus norvegicus	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
designed Fab light chain	B [auth L]	215	Rattus norvegicus	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
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain F [auth H] MOL2 format, chain F [auth H] mmCIF format, chain F [auth H]	F [auth H]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain F [auth H] Interactions & Density Focus chain F [auth H]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain C [auth H] SDF format, chain I [auth L] MOL2 format, chain C [auth H] MOL2 format, chain I [auth L] mmCIF format, chain C [auth H] mmCIF format, chain I [auth L]	C [auth H], I [auth L]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain C [auth H] Focus chain I [auth L] Interactions & Density Focus chain C [auth H] Focus chain I [auth L]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain D [auth H] SDF format, chain G [auth L] SDF format, chain H [auth L] MOL2 format, chain D [auth H] MOL2 format, chain G [auth L] MOL2 format, chain H [auth L] mmCIF format, chain D [auth H] mmCIF format, chain G [auth L] mmCIF format, chain H [auth L]	D [auth H], G [auth L], H [auth L]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth H] Focus chain G [auth L] Focus chain H [auth L] Interactions & Density Focus chain D [auth H] Focus chain G [auth L] Focus chain H [auth L]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain E [auth H] MOL2 format, chain E [auth H] mmCIF format, chain E [auth H]	E [auth H]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth H] Interactions & Density Focus chain E [auth H]