Download MendeleyMulti-Temperature Crystallography of S-Adenosylmethionine Decarboxylase Observes Dynamic Loop Motions
Patel, J.R., Bonzon, T.J., Bakht, T.F., Fagbohun, O.O., Clinger, J.A.(2025) Biomolecules 15
9PBB | pdb_00009pbb
293K human S-adenosylmethionine decarboxylase
- PDB DOI: https://doi.org/10.2210/pdb9PBB/pdb
- Classification: LYASE
- Organism(s): Homo sapiens
- Expression System: Escherichia coli BL21
- Mutation(s): No
- Deposited: 2025-06-26 Released: 2025-09-17
- Funding Organization(s): Cancer Prevention and Research Institute of Texas (CPRIT)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.17 Å
- R-Value Free: 0.223 (Depositor), 0.223 (DCC)
- R-Value Work: 0.208 (Depositor), 0.208 (DCC)
- R-Value Observed: 0.209 (Depositor)
Starting Model: experimental
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This is version 1.0 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-adenosylmethionine decarboxylase beta chain | A [auth B] | 80 | Homo sapiens | Mutation(s): 0 Gene Names: AMD1, AMD EC: 4.1.1.50 |  |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P17707 (Homo sapiens) Explore P17707 Go to UniProtKB: P17707 | |||||
PHAROS: P17707 GTEx: ENSG00000123505 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P17707 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| S-adenosylmethionine decarboxylase alpha chain | B [auth A] | 267 | Homo sapiens | Mutation(s): 0 Gene Names: AMD1, AMD EC: 4.1.1.50 |  |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P17707 (Homo sapiens) Explore P17707 Go to UniProtKB: P17707 | |||||
PHAROS: P17707 GTEx: ENSG00000123505 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P17707 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| TRS Query on TRS | C [auth A] | 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O |  | ||
| PUT (Subject of Investigation/LOI) Query on PUT | D [auth A] | 1,4-DIAMINOBUTANE C4 H12 N2 KIDHWZJUCRJVML-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.17 Å
- R-Value Free: 0.223 (Depositor), 0.223 (DCC)
- R-Value Work: 0.208 (Depositor), 0.208 (DCC)
- R-Value Observed: 0.209 (Depositor)
Space Group: C 1 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 97.418 | α = 90 |
| b = 45.876 | β = 104.971 |
| c = 72.248 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| Aimless | data scaling |
| xia2 | data reduction |
| PDB_EXTRACT | data extraction |
| PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2025-09-17 Deposition Author(s): Patel, J.R., Bonzon, T.J., Bahkt, T., Fagbohun, O.O., Clinger, J.A.
| Funding Organization | Location | Grant Number |
|---|---|---|
| Cancer Prevention and Research Institute of Texas (CPRIT) | United States | RR220081 |
Revision History (Full details and data files)
- Version 1.0: 2025-09-17
Type: Initial release
