5F71 | pdb_00005f71

Human T-cell immunoglobulin and mucin domain protein 3 (hTIM-3)

• PDB DOI: https://doi.org/10.2210/pdb5F71/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2015-12-07 Released: 2016-02-03 
• Deposition Author(s): Gao, G.F., Lu, G., Wang, H., Qi, J.
• Funding Organization(s): National Natural Science Foundation of China, Strategic Priority Research Program of the Chinese Academy of Sciences

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.257 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.215 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Starting Model: experimental

Literature

Crystal structures of human TIM members: Ebolavirus entry-enhancing receptors

Wang, H., Qi, J.X., Liu, N.N.

(2015) Chin Sci Bull 60: 3438-3453

• DOI: https://doi.org/10.1360/N972015-01255

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 24.64 kDa 
• Atom Count: 1,789 
• Modeled Residue Count: 218 
• Deposited Residue Count: 218 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hepatitis A virus cellular receptor 2	A, B	109	Homo sapiens	Mutation(s): 0  Gene Names: TIMD3 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TDQ0 (Homo sapiens) Explore Q8TDQ0  Go to UniProtKB:  Q8TDQ0
PHAROS:  Q8TDQ0 GTEx:  ENSG00000135077

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	C [auth A], D [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.257 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.215 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.997	α = 90
b = 61.957	β = 90
c = 67.152	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data processing
SCALEPACK	data scaling
PHASER	phasing
Coot	model building
PHENIX	refinement
HKL-2000	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-02-03 
Deposition Author(s): Gao, G.F., Lu, G., Wang, H., Qi, J.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	81590761
Strategic Priority Research Program of the Chinese Academy of Sciences	China	XDB08020100

Revision History  

• Version 1.0: 2016-02-03
  Type: Initial release
  
• Version 1.1: 2017-02-08
  Changes: Source and taxonomy
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-10-30
  Changes: Structure summary