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Firestone, R.S., Cameron, S.A., Karp, J.M., Arcus, V.L., Schramm, V.L.To be published.
5TC8
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
- Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.80 ?
- R-Value Free: 0.180
- R-Value Work: 0.160
- R-Value Observed: 0.161
Starting Model: experimental
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This is version 1.3 of the entry. See complete history.
Literature
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 | 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 AnnotationsExpand | |||||
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Small Molecules
| Ligands 6 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| 2PE Query on 2PE | G [auth A] | NONAETHYLENE GLYCOL C18 H38 O10 YZUUTMGDONTGTN-UHFFFAOYSA-N |  | ||
| TDI Query on 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 Query on PEG | H [auth A], I [auth A] | DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N |  | ||
| PO4 Query on PO4 | C [auth A] | PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K |  | ||
| CL Query on CL | F [auth A] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | ||
| MG Query on MG | D [auth A], E [auth A] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.80 ?
- R-Value Free: 0.180
- R-Value Work: 0.160
- R-Value Observed: 0.161
- Space Group: P 3 2 1
Unit Cell:
| Length ( ? ) | Angle ( ? ) |
|---|---|
| a = 123.065 | α = 90 |
| b = 123.065 | β = 90 |
| c = 44.755 | γ = 120 |
| Software Name | Purpose |
|---|---|
| DENZO | data reduction |
| SCALEPACK | data scaling |
| PHASER | phasing |
| Coot | model building |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
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.
| 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
