PDB-9p1h: 100K human S-adenosylmethionine decarboxylase

ID or keywords:

Entry

Database: PDB / ID: 9p1h

Title

100K human S-adenosylmethionine decarboxylase

Components

(S-adenosylmethionine decarboxylase ...) x 2

Keywords

LYASE / polyamine biosynthesis / decarboxylase / AdoMet

Function / homology

Function and homology information

spermine biosynthetic process / adenosylmethionine decarboxylase / adenosylmethionine decarboxylase activity / Metabolism of polyamines / polyamine metabolic process / putrescine binding / spermidine biosynthetic process / identical protein binding / cytosol
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

FOURIER SYNTHESIS / Resolution: 1.81 Å

Authors

Patel, J.R. / Bonzon, T.J. / Bahkt, T. / Fagbohun, O.O. / Clinger, J.A.

Funding support

United States, 1items

Citation

Journal: Biomolecules / Year: 2025
Title: Multi-Temperature Crystallography of S-Adenosylmethionine Decarboxylase Observes Dynamic Loop Motions.
Authors: Patel, J.R. / Bonzon, T.J. / Bakht, T.F. / Fagbohun, O.O. / Clinger, J.A.

History

Deposition	Jun 10, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 17, 2025	Provider: repository / Type: Initial release
Revision 1.1	Oct 8, 2025	Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9p1h.cif.gz	420.1 KB	Display	PDBx/mmCIF format
PDB format	pdb9p1h.ent.gz	314 KB	Display	PDB format
PDBx/mmJSON format	9p1h.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9p1h_validation.pdf.gz	869.7 KB	Display	wwPDB validaton report
Full document	9p1h_full_validation.pdf.gz	876 KB	Display
Data in XML	9p1h_validation.xml.gz	32.8 KB	Display
Data in CIF	9p1h_validation.cif.gz	44.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/p1/9p1h ftp://data.pdbj.org/pub/pdb/validation_reports/p1/9p1h	HTTPS FTP

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Related structure data

Related structure data	9p7qC 9pbbC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Experimental dataset #1	Data reference: 10.15785/SBGRID/1188 / Data set type: diffraction image data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: S-adenosylmethionine decarboxylase alpha chain

B: S-adenosylmethionine decarboxylase beta chain

D: S-adenosylmethionine decarboxylase beta chain

C: S-adenosylmethionine decarboxylase alpha chain

hetero molecules

80.8 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: S-adenosylmethionine decarboxylase alpha chain

B: S-adenosylmethionine decarboxylase beta chain

hetero molecules

defined by author&software
Evidence: gel filtration
40.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: S-adenosylmethionine decarboxylase beta chain

C: S-adenosylmethionine decarboxylase alpha chain

hetero molecules

defined by author&software
Evidence: gel filtration
40.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	73.855, 55.946, 99.247
Angle α, β, γ (deg.)	90.000, 110.882, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

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S-adenosylmethionine decarboxylase ... , 2 types, 4 molecules ACBD

#1: Protein	S-adenosylmethionine decarboxylase alpha chain Mass: 30685.988 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AMD1, AMD / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P17707
#2: Protein	S-adenosylmethionine decarboxylase beta chain Mass: 9375.358 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AMD1, AMD / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P17707

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Non-polymers , 4 types, 369 molecules

#3: Chemical	ChemComp-PUT / 1,4-DIAMINOBUTANE / PUTRESCINE Mass: 88.151 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₂N₂ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₂NO₃ / Comment: pH buffer*YM
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 362 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.39 Å³/Da / Density % sol: 48.45 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 4mg/mL enzyme in 200mM NaCl 50mM HEPES pH 7.5 1:1 to reservoir solution containing 4-8% PEG 8000 and 50mM Tris-HCl pH 8.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.97946 Å
Detector	Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 20, 2025
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97946 Å / Relative weight: 1
Reflection	Resolution: 1.81→43.48 Å / Num. obs: 67064 / % possible obs: 96.9 % / Redundancy: 3.4 % / B_iso Wilson estimate: 26.81 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.074 / R_pim(I) all: 0.047 / R_rim(I) all: 0.088 / Χ²: 0.79 / Net I/σ(I): 9.4 / Num. measured all: 225636
Reflection shell	Resolution: 1.81→1.86 Å / Redundancy: 3.4 % / R_merge(I) obs: 1.671 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 5042 / CC_1/2: 0.301 / R_pim(I) all: 1.054 / R_rim(I) all: 1.983 / Χ²: 0.58 / % possible all: 98

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Processing

Software

Name	Version	Classification
PHENIX	1.21.2_5419	refinement
Aimless		data scaling
xia2		data reduction
PDB_EXTRACT		data extraction
PHASER		phasing

Refinement

Method to determine structure:

FOURIER SYNTHESIS / Resolution: 1.81→43.46 Å / SU ML: 0.2018 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.1654
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1993	3370	5.03 %
R_work	0.1806	63588	-
obs	0.1816	66958	96.15 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 35.86 Å²

Refinement step

Cycle: LAST / Resolution: 1.81→43.46 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4953	0	56	362	5371

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0069	5129
X-RAY DIFFRACTION	f_angle_d	0.8159	6910
X-RAY DIFFRACTION	f_chiral_restr	0.0498	744
X-RAY DIFFRACTION	f_plane_restr	0.0086	877
X-RAY DIFFRACTION	f_dihedral_angle_d	15.0591	1884

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.81-1.83	0.3063	119	0.3194	2407	X-RAY DIFFRACTION	88.66
1.83-1.86	0.3322	159	0.3089	2647	X-RAY DIFFRACTION	96.46
1.86-1.89	0.2957	151	0.2824	2655	X-RAY DIFFRACTION	98.04
1.89-1.92	0.2826	137	0.2661	2674	X-RAY DIFFRACTION	97.33
1.92-1.95	0.2592	141	0.2471	2668	X-RAY DIFFRACTION	97.26
1.95-1.99	0.2701	133	0.2283	2650	X-RAY DIFFRACTION	97.41
1.99-2.03	0.2041	133	0.2111	2681	X-RAY DIFFRACTION	96.83
2.03-2.07	0.2122	119	0.212	2664	X-RAY DIFFRACTION	96.46
2.07-2.11	0.2478	147	0.21	2631	X-RAY DIFFRACTION	95.63
2.11-2.16	0.2277	128	0.2001	2314	X-RAY DIFFRACTION	84.7
2.16-2.22	0.2107	141	0.1874	2676	X-RAY DIFFRACTION	98.05
2.22-2.28	0.2236	130	0.1755	2685	X-RAY DIFFRACTION	97.64
2.28-2.34	0.2274	130	0.1759	2711	X-RAY DIFFRACTION	98.1
2.34-2.42	0.1905	156	0.1731	2710	X-RAY DIFFRACTION	99.03
2.42-2.51	0.1837	158	0.1775	2707	X-RAY DIFFRACTION	98.32
2.51-2.61	0.1916	160	0.1846	2680	X-RAY DIFFRACTION	98.3
2.61-2.72	0.2075	155	0.1853	2693	X-RAY DIFFRACTION	98.31
2.72-2.87	0.1977	138	0.1851	2716	X-RAY DIFFRACTION	98.18
2.87-3.05	0.2129	132	0.1794	2534	X-RAY DIFFRACTION	92.15
3.05-3.28	0.1974	127	0.1702	2595	X-RAY DIFFRACTION	93.03
3.28-3.61	0.1761	160	0.1605	2735	X-RAY DIFFRACTION	99.28
3.61-4.14	0.1725	126	0.1465	2778	X-RAY DIFFRACTION	98.94
4.14-5.21	0.1455	158	0.1393	2740	X-RAY DIFFRACTION	98.04
5.21-43.46	0.2154	132	0.198	2637	X-RAY DIFFRACTION	91.63

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	1.93940092637	-0.210745577111	-0.17632404057	2.98975610689	-0.368819350152	2.72407589398	0.118139421662	0.208375656049	-0.119879912622	-0.090504404088	-0.0412671271737	0.0475428666828	-0.0383061374714	-0.0316224115015	-0.0489254576098	0.224283051316	0.0138137486092	-0.00871955230214	0.181688339268	-0.0159921644672	0.203288160851	37.7953216731	2.38437500601	-46.2771625663
2	1.86207703307	-0.15765188671	-0.656198705012	1.61092628432	-1.14605737491	5.2643977918	-0.0639827271769	0.492916651919	-0.454694354281	-0.379874568371	-0.0923111916726	-0.151951478227	0.51414622649	0.313653367047	0.142710609142	0.384943859738	0.0510080353693	0.0453735401574	0.341761197145	-0.0837158939764	0.282216716988	46.7085384083	-4.22394941128	-50.824664309
3	2.43726875552	-0.0504171011663	0.879277660769	1.24667525511	0.0611077583194	1.74508760153	0.0269569278853	-0.199932583072	-0.324396438085	-0.0397213902981	-0.0351609697602	-0.0327179912035	0.223514598595	0.154100429845	0.00588104717142	0.219017589512	0.0151709055745	-0.000574465775127	0.154267210034	0.00405541143466	0.218810525567	44.1438760521	-1.27990120529	-33.2158394029
4	2.66155621328	-0.212811163855	0.144407121277	1.90245625926	-0.082259351877	1.81802068815	0.0131667301711	-0.0372202468148	0.187356564068	-0.121686774989	-0.111534532909	-0.0841810165032	-0.168163929293	0.235023563836	0.0755653404645	0.215997076678	-0.0150161805593	-0.000704770368554	0.160011039449	0.00801465093597	0.176148043864	35.9548845522	10.9577829145	-37.3330478257
5	3.30448797922	0.303452892528	0.339274533939	3.4642946667	0.534648017923	3.59414898695	0.0278105628484	-0.0190136483321	-0.0098379048793	-0.750755260362	0.096890997669	0.908268797023	0.111876657781	-0.714210117523	-0.0714388617479	0.331349639233	-0.0170937651583	-0.123984618427	0.336291369877	0.0340859317304	0.479857256335	12.117107607	6.4979790271	-44.9813468251
6	2.4035486361	0.246281129289	0.152665931659	1.57134179341	-0.597084256045	2.57375109808	-0.0155626832033	0.0107022403695	0.294914405807	-0.0851888962097	-0.022855200384	0.246385091707	-0.151264209528	-0.113603345693	0.0500699209364	0.19591914537	0.0115728166954	-0.024201652866	0.127938404278	-0.0119417591297	0.261079329395	25.7589226357	11.3224026435	-40.537931149
7	4.70318750403	0.565454331621	-1.53760348978	1.25648518561	-0.00802966821465	2.41509567056	0.081301461013	-0.254090043552	0.970620591869	0.114062967259	0.0105819086478	0.280524970296	-0.498381759934	0.0963075141213	-0.0913400138811	0.28785349678	-0.0144476637689	-0.0142271846191	0.20374338726	-0.0387557952633	0.3341358119	34.9543602272	17.1450289944	-31.0841004742
8	4.64281291791	0.0622611697876	-0.652985557128	3.33145452237	0.22710543147	3.52656218853	0.0613220904353	-0.791291434726	0.380665137671	0.236177746541	-0.134837067815	0.0774931900487	-0.274662197568	0.149169971336	0.0368319875099	0.224547885276	0.00386636443601	-0.0395990599568	0.233331256623	-0.0432656203085	0.219893921093	38.4240089585	14.0270893615	-26.3008322042
9	1.1015921469	-0.0561903406783	0.559122752383	1.23312651066	-0.0286974457004	1.3942104175	0.0307421207239	0.136503946154	-0.0709765589406	-0.232111815485	-0.0098963768056	-0.0349857469872	0.0899036273313	0.328748861443	-0.00802420123628	0.24297308717	0.0184889947626	0.0079491527851	0.223023562538	-0.0115833213006	0.19573275311	40.700030316	2.57288368338	-47.1826640167
10	2.6542271166	0.272428063977	-0.378000709228	2.84542348621	-0.318066286625	5.45816387875	0.078096793206	0.403452715956	-0.728132312363	-0.491479026387	-0.19619952576	0.136739558859	0.335639413711	0.103425850762	0.111124250634	0.323881640357	0.0240033293653	0.0172761063468	0.306513452996	-0.12394267448	0.315040547534	36.9538642787	-7.0721072915	-53.667484407
11	3.7597367867	-0.00126677312786	0.422755861127	4.20295504669	0.0510361853103	2.23727281547	0.0861158914908	0.329488669841	-0.375034623074	-0.151871109622	-0.105571063937	0.0416472673601	-0.0223363386057	0.0672365029031	0.0190865688656	0.267202323138	0.00889505520276	-0.0682394459677	0.223429973511	-0.0257057547711	0.248810430862	31.4160264862	2.31888377989	-52.1314576671
12	1.46235301864	0.293972157059	-0.401371535232	0.488996250739	-0.0984742989182	1.40007927061	0.174716451586	-0.658275237616	-0.322054105692	0.276787931278	-0.20267357095	0.0985357716709	0.072494823273	-0.32869323622	0.0525180873809	0.376042648938	-0.0611225160248	-0.0010823305032	0.591948863956	0.0643546152779	0.243755837274	52.6289938065	3.26370961748	3.38507503898
13	4.92607095423	-1.07958089857	-0.938982721563	6.38504816299	-0.0595533384036	2.53740433863	0.00352043713026	-1.19198711302	-0.267475810255	0.318263139069	-0.041259030169	0.0393382473473	-0.184827420463	-0.282678220442	0.0468549723978	0.36186971903	-0.0325242710152	-0.0259466471964	0.629786713131	0.0280061442716	0.25394661837	59.9272724691	7.73329057035	6.5454538334
14	2.61209989599	0.0947815938065	-1.08389482599	3.29947422124	0.934172206647	3.08248895494	0.198400323264	-0.761807613932	0.0551013795993	0.225982990897	-0.0758055208607	0.0455491639845	-0.119543522036	-0.349094257314	-0.103878192602	0.269428873022	-0.0195999730131	0.0202371214284	0.507268774993	0.0215018714012	0.206711212774	53.7325128619	6.02946757726	0.255433596509
15	0.946756914103	-0.0704685675444	-0.569930091988	0.460561994002	1.13656483009	3.03914938134	0.0387845281247	-0.736565608956	-0.132031608306	0.644119852376	0.0231679341135	0.398984408661	0.274115790446	-0.536897865079	0.418457857415	0.417664206292	-0.136229018566	0.133856057865	0.793896594039	0.216924499043	0.231496334153	44.6866774318	0.373682329228	5.80531925591
16	2.70266917407	0.123711310358	1.14608464348	1.51442215323	0.0240327657988	2.20605417978	0.150563072114	-0.26080940463	-0.488447584553	0.107843774401	-0.0987078157653	0.160596550956	0.237957916933	-0.340712479089	-0.0192225786033	0.206156711079	-0.053958578848	0.00556403797681	0.23101531133	0.0332291139669	0.235287247783	47.3200294496	0.477037665995	-12.1492290624
17	1.38128527072	0.76028836172	0.522974979319	1.52695219511	-0.31920802833	1.10652350651	-0.150921253648	-0.25793417818	0.224826122672	0.12449706024	0.0142039596812	0.0544956465475	-0.0993181537718	0.00203177544142	0.136512104804	0.221813797036	0.0311070521442	-0.0165716836526	0.242357599655	-0.0386603695042	0.189553523771	57.8851642471	12.2385247924	-10.6790365555
18	2.79774267986	-0.507524325596	0.301145502657	3.07045202375	-0.889958756459	2.98766174751	-0.00032895051674	-0.224750218111	-0.0672612432116	0.710889375676	-0.175049123412	-0.902549417428	-0.132181959962	0.735924125802	0.174253741073	0.351915766699	-0.0406474894112	-0.15913842593	0.434369167393	0.0522992206102	0.483849356665	79.4236457814	9.23136844661	-1.49416585305
19	2.17493745382	-0.846601465744	-0.540980937561	2.8662365328	0.428186449307	2.27625320199	-0.171616183192	-0.545191633022	0.409337376604	0.360815072394	-0.0412322108623	-0.370051684127	-0.235182466612	0.256588093584	0.177957663265	0.317137486321	-0.0313093340247	-0.101861160916	0.350373002401	-0.0330767841208	0.3204966811	69.8680116195	16.3446980059	-1.50252904117
20	3.15211529633	0.324605427492	0.768530571871	1.44235784279	0.425411752768	2.77050810728	-0.0582026363846	-0.0768081994932	0.256321709893	-0.0249120015217	-0.043638236962	-0.17866998308	-0.152552263037	0.0616040798604	0.103179017645	0.200435041497	-0.00773566072688	-0.0148700206523	0.183628706676	-0.00383824679212	0.18087426226	63.8074455487	12.9916191409	-9.73064600382
21	1.99792887449	0.231587345444	0.453110336362	1.20470867707	0.302506950457	1.41994006691	-0.187430840334	0.123576383121	0.67281601193	-0.0448179532617	-0.0828742571793	0.090884517415	-0.294769721656	-0.135572152827	0.208825893936	0.352302506992	-0.0090735171614	-0.0530675751313	0.322944221881	0.0534278099744	0.354894122108	54.3525057665	17.7172867772	-21.5054750291
22	3.32340573101	-0.0477334108979	-0.423668375825	3.31346519181	0.243312854798	3.12770796864	-0.237730231237	-0.119745864183	0.281497673093	-0.0819372414086	0.000215981138614	0.187370727779	-0.120355978862	-0.0282127469661	0.193141389619	0.223236597945	0.00624541859073	-0.0214394468923	0.209339285495	-0.00934200584281	0.237696980586	53.2794497275	14.4886630645	-19.3418206221

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 69 through 86 )	A	B	69 - 86	2 - 19
2	2	chain 'A' and (resid 87 through 102 )	A	B	87 - 102	20 - 35
3	3	chain 'A' and (resid 103 through 162 )	A	B	103 - 162	36 - 95
4	4	chain 'A' and (resid 163 through 192 )	A	B	163 - 192	96 - 125
5	5	chain 'A' and (resid 193 through 206 )	A	B	193 - 206	126 - 139
6	6	chain 'A' and (resid 207 through 275 )	A	B	207 - 275	140 - 208
7	7	chain 'A' and (resid 276 through 304 )	A	B	276 - 304	209 - 231
8	8	chain 'A' and (resid 305 through 329 )	A	B	305 - 329	232 - 256
9	9	chain 'B' and (resid 6 through 36 )	B	H	6 - 36	1 - 24
10	10	chain 'B' and (resid 37 through 47 )	B	H	37 - 47	25 - 35
11	11	chain 'B' and (resid 48 through 67 )	B	H	48 - 67	36 - 55
12	12	chain 'D' and (resid 6 through 47 )	D	I	6 - 47	1 - 34
13	13	chain 'D' and (resid 48 through 66 )	D	I	48 - 66	35 - 53
14	14	chain 'C' and (resid 69 through 86 )	C	L	69 - 86	2 - 19
15	15	chain 'C' and (resid 87 through 102 )	C	L	87 - 102	20 - 35
16	16	chain 'C' and (resid 103 through 162 )	C	L	103 - 162	36 - 95
17	17	chain 'C' and (resid 163 through 192 )	C	L	163 - 192	96 - 125
18	18	chain 'C' and (resid 193 through 206 )	C	L	193 - 206	126 - 139
19	19	chain 'C' and (resid 207 through 222 )	C	L	207 - 222	140 - 155
20	20	chain 'C' and (resid 223 through 287 )	C	L	223 - 287	156 - 220
21	21	chain 'C' and (resid 288 through 315 )	C	L	288 - 315	221 - 241
22	22	chain 'C' and (resid 316 through 328 )	C	L	316 - 328	242 - 254

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S-adenosylmethionine decarboxylase ... , 2 types, 4 molecules ACBD

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