5TC8 | pdb_00005tc8

Crystal structure of human 5'-deoxy-5'-methylthioadenosine phosphorylase in complex with methylthio-DADMe-Immucillin-A

• PDB DOI: https://doi.org/10.2210/pdb5TC8/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-09-14 Released: 2017-10-11 
• Deposition Author(s): Cameron, S.A., Firestone, R.S., Schramm, V.L., Almo, S.C.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.180 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.160 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.161 (Depositor) 

Starting Model: experimental

Literature

TBA

Firestone, R.S., Cameron, S.A., Karp, J.M., Arcus, V.L., Schramm, V.L.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content 

• Total Structure Weight: 34.22 kDa 
• Atom Count: 2,381 
• Modeled Residue Count: 273 
• Deposited Residue Count: 297 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
S-methyl-5'-thioadenosine phosphorylase	A	297	Homo sapiens	Mutation(s): 0  Gene Names: MTAP, MSAP EC: 2.4.2.28
UniProt & NIH Common Fund Data Resources
Find proteins for Q13126 (Homo sapiens) Explore Q13126  Go to UniProtKB:  Q13126
PHAROS:  Q13126 GTEx:  ENSG00000099810

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2PE	G [auth A]	NONAETHYLENE GLYCOL C18 H38 O10 YZUUTMGDONTGTN-UHFFFAOYSA-N
TDI	B [auth A]	(3R,4S)-1-[(4-AMINO-5H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)METHYL]-4-[(METHYLSULFANYL)METHYL]PYRROLIDIN-3-OL C13 H19 N5 O S NTHMDFGHOCNNOE-ZJUUUORDSA-N
PEG	H [auth A], I [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
PO4	C [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
CL	F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	D [auth A], E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
TDI	BindingDB:  5TC8	Ki: min: 0.08, max: 1.7 (nM) from 4 assay(s)
		Kd: min: 0.03, max: 0.09 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.180 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.160 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.161 (Depositor) 

Space Group: P 3 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 123.065	α = 90
b = 123.065	β = 90
c = 44.755	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
Coot	model building
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-10-11 
Deposition Author(s): Cameron, S.A., Firestone, R.S., Schramm, V.L., Almo, S.C.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	6-RO1-CA135405-08

Revision History  

• Version 1.0: 2017-10-11
  Type: Initial release
  
• Version 1.1: 2019-12-04
  Changes: Author supporting evidence
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-11-13
  Changes: Structure summary