9ILF | pdb_00009ilf

Crystal structure of human malectin in complex with nigerose.

• PDB DOI: https://doi.org/10.2210/pdb9ILF/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia
• Mutation(s): No 


• Deposited: 2024-06-29 Released: 2025-07-02 
• Deposition Author(s): Si, Y.L.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.56 Å
• R-Value Free: 
  0.194 (Depositor), 0.198 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.176 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

Starting Model: experimental

Literature

The Structural Basis of Human Malectin Recognition of Ligands

Si, Y.L.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 42.56 kDa 
• Atom Count: 3,438 
• Modeled Residue Count: 368 
• Deposited Residue Count: 368 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Malectin	A, B	184	Homo sapiens	Mutation(s): 0  Gene Names: MLEC, KIAA0152
UniProt & NIH Common Fund Data Resources
Find proteins for Q14165 (Homo sapiens) Explore Q14165  Go to UniProtKB:  Q14165
PHAROS:  Q14165 GTEx:  ENSG00000110917

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose	C, D	2		N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	F [auth A], H [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
DIO	E [auth A], G [auth B]	1,4-DIETHYLENE DIOXIDE C4 H8 O2 RYHBNJHYFVUHQT-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.56 Å
• R-Value Free:  0.194 (Depositor), 0.198 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.176 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.267	α = 90
b = 100.267	β = 90
c = 36.004	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPX	data processing
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-02 
Deposition Author(s): Si, Y.L.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	82201916

Revision History  

• Version 1.0: 2025-07-02
  Type: Initial release