5F7H | pdb_00005f7h

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

PDB DOI: https://doi.org/10.2210/pdb5F7H/pdb

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 (Depositor), 0.280 (DCC)
R-Value Work:
0.210 (Depositor), 0.210 (DCC)
R-Value Observed:
0.213 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 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

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

Macromolecule Content

Total Structure Weight: 77.36 kDa
Atom Count: 5,468
Modeled Residue Count: 674
Deposited Residue Count: 678
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
T-cell immunoglobulin and mucin domain-containing protein 4	A [auth B] B [auth A] C D E A [auth B], B [auth A], C, D, E, F	113	Homo sapiens	Mutation(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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q96H15
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SEP Query on SEP Download Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain J [auth A] SDF format, chain L [auth C] SDF format, chain N [auth D] SDF format, chain P [auth E] SDF format, chain R [auth F] MOL2 format, chain H [auth B] MOL2 format, chain J [auth A] MOL2 format, chain L [auth C] MOL2 format, chain N [auth D] MOL2 format, chain P [auth E] MOL2 format, chain R [auth F] mmCIF format, chain H [auth B] mmCIF format, chain J [auth A] mmCIF format, chain L [auth C] mmCIF format, chain N [auth D] mmCIF format, chain P [auth E] mmCIF format, chain R [auth F]	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		Interactions Focus chain H [auth B] Focus chain J [auth A] Focus chain L [auth C] Focus chain N [auth D] Focus chain P [auth E] Focus chain R [auth F] Interactions & Density Focus chain H [auth B] Focus chain J [auth A] Focus chain L [auth C] Focus chain N [auth D] Focus chain P [auth E] Focus chain R [auth F]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain I [auth A] SDF format, chain K [auth C] SDF format, chain M [auth D] SDF format, chain O [auth E] SDF format, chain Q [auth F] MOL2 format, chain G [auth B] MOL2 format, chain I [auth A] MOL2 format, chain K [auth C] MOL2 format, chain M [auth D] MOL2 format, chain O [auth E] MOL2 format, chain Q [auth F] mmCIF format, chain G [auth B] mmCIF format, chain I [auth A] mmCIF format, chain K [auth C] mmCIF format, chain M [auth D] mmCIF format, chain O [auth E] mmCIF format, chain Q [auth F]	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		Interactions Focus chain G [auth B] Focus chain I [auth A] Focus chain K [auth C] Focus chain M [auth D] Focus chain O [auth E] Focus chain Q [auth F] Interactions & Density Focus chain G [auth B] Focus chain I [auth A] Focus chain K [auth C] Focus chain M [auth D] Focus chain O [auth E] Focus chain Q [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.278 (Depositor), 0.280 (DCC)
R-Value Work: 0.210 (Depositor), 0.210 (DCC)
R-Value Observed: 0.213 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 212.444	α = 90
b = 65.034	β = 108.55
c = 68.851	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

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2016-02-03

Deposition Author(s):

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 (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
Version 1.2: 2024-11-13
Changes: Structure summary

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Help and Resources

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

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

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations