5F7H

Human T-cell immunoglobulin and mucin domain protein 4 (hTIM-4) complex with phosphoserine

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

  • Deposited: 2015-12-08 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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.213 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history. 


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


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
T-cell immunoglobulin and mucin domain-containing protein 4113Homo sapiensMutation(s): 0 
Gene Names: TIMD4, TIM4
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q96H15 (Homo sapiens)
Explore Q96H15 
Go to UniProtKB:  Q96H15
PHAROS:  Q96H15
GTEx:  ENSG00000145850 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96H15
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SEP
Query on SEP
Download Ideal Coordinates CCD File 
H [auth B]
J [auth A]
L [auth C]
N [auth D]
P [auth E]
H [auth B],
J [auth A],
L [auth C],
N [auth D],
P [auth E],
R [auth F]
PHOSPHOSERINE
C3 H8 N O6 P
BZQFBWGGLXLEPQ-REOHCLBHSA-N
CA
Query on CA
Download Ideal Coordinates CCD File 
G [auth B]
I [auth A]
K [auth C]
M [auth D]
O [auth E]
G [auth B],
I [auth A],
K [auth C],
M [auth D],
O [auth E],
Q [auth F]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.213 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 212.444α = 90
b = 65.034β = 108.55
c = 68.851γ = 90
Software Package:
Software NamePurpose
HKL-2000data processing
SCALEPACKdata scaling
PHASERphasing
Cootmodel building
PHENIXrefinement
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina81590761
Strategic Priority Research Program of the Chinese Academy of SciencesChinaXDB08020100

Revision History  (Full details and data files)

  • Version 1.0: 2016-02-03
    Type: Initial release
  • Version 1.1: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description