5TC6 | pdb_00005tc6

Crystal structure of human 5'-deoxy-5'-methylthioadenosine phosphorylase in complex with propylthio-immucillin-A

PDB DOI: https://doi.org/10.2210/pdb5TC6/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: 1.48 Å
R-Value Free:
0.185 (Depositor), 0.180 (DCC)
R-Value Work:
0.167 (Depositor), 0.170 (DCC)
R-Value Observed:
0.168 (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: 33.69 kDa
Atom Count: 2,432
Modelled Residue Count: 273
Deposited Residue Count: 297
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q13126
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
7A6 Query on 7A6 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]	(2S,3S,4R,5S)-2-(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)-5-[(propylsulfanyl)methyl]pyrrolidine-3,4-diol C₁₄ H₂₁ N₅ O₂ S SMSLFFRQRVMFGA-LGOOBZPGSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [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]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [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]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
7A6	BindingDB: 5TC6	Ki: min: 0.21, max: 4 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.48 Å
R-Value Free: 0.185 (Depositor), 0.180 (DCC)
R-Value Work: 0.167 (Depositor), 0.170 (DCC)
R-Value Observed: 0.168 (Depositor)

Space Group: P 3 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 122.76	α = 90
b = 122.76	β = 90
c = 44.484	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

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, Refinement description
Version 1.3: 2024-11-13
Changes: Structure summary