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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.180 (Depositor), 0.189 (DCC)
R-Value Work:
0.160 (Depositor), 0.173 (DCC)
R-Value Observed:
0.161 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

TBA

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

To be published.

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

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q13126
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
2PE Query on 2PE Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	NONAETHYLENE GLYCOL C₁₈ H₃₈ O₁₀ YZUUTMGDONTGTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
TDI Query on TDI Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	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		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A]	H [auth A], I [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain H [auth A] Focus chain I [auth A]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	D [auth A], E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.180 (Depositor), 0.189 (DCC)
R-Value Work: 0.160 (Depositor), 0.173 (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

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2017-10-11

Deposition Author(s):

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

Revision History (Full details and data files)

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

5TC8 | pdb_00005tc8

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

Literature

TBA

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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