9GO4 | pdb_00009go4

Structural characterization of citrate-binding site in human RNase2

PDB DOI: https://doi.org/10.2210/pdb9GO4/pdb

Classification: PROTEIN BINDING
Organism(s): Escherichia coli 'BL21-Gold(DE3)pLysS AG
Expression System: Expression vector pET-mod
Mutation(s): No

Deposited: 2024-09-04 Released: 2026-03-18
Deposition Author(s): Xincheng, K., Jiarui, L., Prats-Ejarque, G., Boix, E.
Funding Organization(s): Agencia Estatal de Investigacion (AEI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.17 Å
R-Value Free:
0.188 (Depositor), 0.186 (DCC)
R-Value Work:
0.151 (Depositor), 0.151 (DCC)
R-Value Observed:
0.153 (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

Structural basis for saccharide binding by human RNase 2/EDN, a protein combining enzymatic and lectin properties

Kang, X., Prats-Ejarque, G., Boix, E., Li, J.

(2026) bioRxiv

DOI: https://doi.org/10.64898/2026.03.20.713198

Macromolecule Content

Total Structure Weight: 16.51 kDa
Atom Count: 1,425
Modeled Residue Count: 135
Deposited Residue Count: 135
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-secretory ribonuclease	A	135	Escherichia coli 'BL21-Gold(DE3)pLysS AG	Mutation(s): 0 Gene Names: RNASE2, EDN, RNS2 EC: 4.6.1.18
UniProt & NIH Common Fund Data Resources
Find proteins for P10153 (Homo sapiens) Explore P10153 Go to UniProtKB: P10153
PHAROS: P10153 GTEx: ENSG00000169385
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P10153
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CIT (Subject of Investigation/LOI) Query on CIT Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain F [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain F [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain F [auth A]	B [auth A], C [auth A], F [auth A]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain F [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain F [auth A]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
ACT Query on ACT 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]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain H [auth A] MOL2 format, chain D [auth A] MOL2 format, chain H [auth A] mmCIF format, chain D [auth A] mmCIF format, chain H [auth A]	D [auth A], H [auth A]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain H [auth A] Interactions & Density Focus chain D [auth A] Focus chain H [auth A]
NA Query on NA 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]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		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]