9N7M | pdb_00009n7m

Designed anti-OSM Fab

PDB DOI: https://doi.org/10.2210/pdb9N7M/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: 2.15 Å
R-Value Free:
0.242 (Depositor), 0.242 (DCC)
R-Value Work:
0.210 (Depositor), 0.210 (DCC)
R-Value Observed:
0.211 (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: 95.78 kDa
Atom Count: 7,474
Modeled Residue Count: 869
Deposited Residue Count: 884
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], C [auth A]	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], D [auth B]	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth H] SDF format, chain M [auth B] SDF format, chain J [auth A] SDF format, chain H [auth L] SDF format, chain F [auth H] MOL2 format, chain E [auth H] MOL2 format, chain M [auth B] MOL2 format, chain J [auth A] MOL2 format, chain H [auth L] MOL2 format, chain F [auth H] mmCIF format, chain E [auth H] mmCIF format, chain M [auth B] mmCIF format, chain J [auth A] mmCIF format, chain H [auth L] mmCIF format, chain F [auth H]	E [auth H], F [auth H], H [auth L], J [auth A], M [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth H] Focus chain F [auth H] Focus chain H [auth L] Focus chain J [auth A] Focus chain M [auth B] Interactions & Density Focus chain E [auth H] Focus chain F [auth H] Focus chain H [auth L] Focus chain J [auth A] Focus chain M [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] MOL2 format, chain K [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] mmCIF format, chain K [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B]	K [auth A], N [auth B], O [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain I [auth L] SDF format, chain L [auth A] SDF format, chain G [auth H] MOL2 format, chain I [auth L] MOL2 format, chain L [auth A] MOL2 format, chain G [auth H] mmCIF format, chain I [auth L] mmCIF format, chain L [auth A] mmCIF format, chain G [auth H]	G [auth H], I [auth L], L [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth H] Focus chain I [auth L] Focus chain L [auth A] Interactions & Density Focus chain G [auth H] Focus chain I [auth L] Focus chain L [auth A]