9P1H | pdb_00009p1h

100K human S-adenosylmethionine decarboxylase

PDB DOI: https://doi.org/10.2210/pdb9P1H/pdb

Classification: LYASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21
Mutation(s): Yes

Deposited: 2025-06-10 Released: 2025-09-17
Deposition Author(s): Patel, J.R., Bonzon, T.J., Bahkt, T., Fagbohun, O.O., Clinger, J.A.
Funding Organization(s): Cancer Prevention and Research Institute of Texas (CPRIT)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.81 Å
R-Value Free:
0.199 (Depositor), 0.199 (DCC)
R-Value Work:
0.181 (Depositor), 0.181 (DCC)
R-Value Observed:
0.182 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Multi-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

DOI: https://doi.org/10.3390/biom15091274

Macromolecule Content

Total Structure Weight: 80.82 kDa
Atom Count: 5,382
Modeled Residue Count: 618
Deposited Residue Count: 694
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
S-adenosylmethionine decarboxylase alpha chain	A, D [auth C]	267	Homo sapiens	Mutation(s): 1 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 Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
S-adenosylmethionine decarboxylase beta chain	B, C [auth D]	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 Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth C] MOL2 format, chain F [auth A] MOL2 format, chain J [auth C] mmCIF format, chain F [auth A] mmCIF format, chain J [auth C]	F [auth A], J [auth C]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain F [auth A] Focus chain J [auth C] Interactions & Density Focus chain F [auth A] Focus chain J [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain K [auth C] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain K [auth C] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain K [auth C]	G [auth A], H [auth A], K [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth C] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth C]
PUT (Subject of Investigation/LOI) Query on PUT Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth C] MOL2 format, chain E [auth A] MOL2 format, chain I [auth C] mmCIF format, chain E [auth A] mmCIF format, chain I [auth C]	E [auth A], I [auth C]	1,4-DIAMINOBUTANE C₄ H₁₂ N₂ KIDHWZJUCRJVML-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth C] Interactions & Density Focus chain E [auth A] Focus chain I [auth C]