9IGO | pdb_00009igo

PR3 S203A I221N W222N G223T mutant in complex with the extracellular domain of CD177

PDB DOI: https://doi.org/10.2210/pdb9IGO/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): Yes

Deposited: 2025-02-19 Released: 2026-02-25
Deposition Author(s): Zheng-Gerard, C., El Omari, K., Seiradake, E.
Funding Organization(s): Wellcome Trust

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.184 (Depositor), 0.184 (DCC)
R-Value Work:
0.146 (Depositor), 0.146 (DCC)
R-Value Observed:
0.148 (Depositor)

Starting Models: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

PR3 S203A I221N W222N G223T mutant in complex with the extracellular domain of CD177

Zheng-Gerard, C., El Omari, K., Seiradake, E., Joha, J., Carrasquero, M., Lowe, E., Dubey, S., Draper, S.J., Lin, H.H., McHugh, K., Salama, A., Chang, Y.C.

To be published.

Macromolecule Content

Total Structure Weight: 49.18 kDa
Atom Count: 3,695
Modeled Residue Count: 404
Deposited Residue Count: 432
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Myeloblastin	A	238	Homo sapiens	Mutation(s): 5 Gene Names: PRTN3, MBN EC: 3.4.21.76
UniProt & NIH Common Fund Data Resources
Find proteins for P24158 (Homo sapiens) Explore P24158 Go to UniProtKB: P24158
PHAROS: P24158 GTEx: ENSG00000196415
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P24158
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain A	Go to GlyGen: P24158-1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CD177 antigen	B	194	Homo sapiens	Mutation(s): 0 Gene Names: CD177, NB1, PRV1, UNQ595/PRO1181
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N6Q3 (Homo sapiens) Explore Q8N6Q3 Go to UniProtKB: Q8N6Q3
PHAROS: Q8N6Q3 GTEx: ENSG00000204936
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8N6Q3
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain B	Go to GlyGen: Q8N6Q3-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, D	2		N-Glycosylation	Interactions Focus chain C Focus chain D Interactions & Density Focus chain C Focus chain D

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A]	E [auth A], F [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain L [auth B] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] mmCIF format, chain H [auth A] mmCIF format, chain L [auth B]	H [auth A], L [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain L [auth B] Interactions & Density Focus chain H [auth A] Focus chain L [auth B]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A]	I [auth A], J [auth A], K [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A]
CL Query on CL 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]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]