9EKD | pdb_00009ekd

Structure of a C1r Zymogen Fragment Bound to SALO

PDB DOI: https://doi.org/10.2210/pdb9EKD/pdb

Classification: IMMUNE SYSTEM,HYDROLASE
Organism(s): Lutzomyia longipalpis, Homo sapiens
Expression System: Homo sapiens
Mutation(s): Yes

Deposited: 2024-12-02 Released: 2025-02-12
Deposition Author(s): Duan, H., Geisbrecht, B.V.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.28 Å
R-Value Free:
0.286 (Depositor), 0.287 (DCC)
R-Value Work:
0.242 (Depositor), 0.242 (DCC)
R-Value Observed:
0.246 (Depositor)

Starting Models: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Complement Evasion by Blocking Activation of the C1r Zymogen

Duan, H., Geisbrecht, B.V.

To be published.

Macromolecule Content

Total Structure Weight: 117.65 kDa
Atom Count: 7,644
Modelled Residue Count: 953
Deposited Residue Count: 1,026
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Salivary anti-complement protein	A, C [auth B]	104	Lutzomyia longipalpis	Mutation(s): 0
UniProt
Find proteins for Q5WPZ4 (Lutzomyia longipalpis) Explore Q5WPZ4 Go to UniProtKB: Q5WPZ4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5WPZ4
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Complement C1r subcomponent	B [auth C], D	409	Homo sapiens	Mutation(s): 1 Gene Names: C1R EC: 3.4.21.41
UniProt & NIH Common Fund Data Resources
Find proteins for P00736 (Homo sapiens) Explore P00736 Go to UniProtKB: P00736
PHAROS: P00736
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00736
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TYS Query on TYS	A, C [auth B]	L-PEPTIDE LINKING	C₉ H₁₁ N O₆ S		TYR

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.28 Å
R-Value Free: 0.286 (Depositor), 0.287 (DCC)
R-Value Work: 0.242 (Depositor), 0.242 (DCC)
R-Value Observed: 0.246 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.831	α = 90
b = 117.831	β = 90
c = 190.582	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
HKL-2000	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-02-12

Deposition Author(s):

Geisbrecht, B.V.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM140852

Revision History (Full details and data files)

Version 1.0: 2025-02-12
Type: Initial release

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.