PDB-9pdh: X-ray structure of WT Drosophila Ahcy bound to NAD and adenosine ...

ID or keywords:

Entry

Database: PDB / ID: 9pdh

Title

X-ray structure of WT Drosophila Ahcy bound to NAD and adenosine at 2.50 A

Components

Adenosylhomocysteinase

Keywords

HYDROLASE / S-adenosylhomocysteinase (Ahcy) / one-carbon metabolism / redox homeostasis / redox-regulation / DESI-MS / retinal degeneration / Drosophila

Function / homology

Function and homology information

Methylation / Sulfur amino acid metabolism / adenosylhomocysteinase / adenosylhomocysteinase activity / S-adenosylmethionine cycle / one-carbon metabolic process / cytosol
Similarity search - Function

Biological species

Drosophila melanogaster (fruit fly)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.5 Å

Authors

Singhal, K. / Mesecar, A.D.

Funding support

United States, 1items

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2025
Title: Drosophila Ahcy is a redox sensor that modulates gene expression to protect against light stress-induced retinal degeneration.
Authors: Stanhope, S.C. / Singhal, K. / Morato, N.M. / Feng, Y. / Meng, G. / Marlin, M.N. / Kotanko, C.C. / Jarrett, M.M. / Mesecar, A.D. / Cooks, R.G. / Weake, V.M.

History

Deposition	Jun 30, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 17, 2025	Provider: repository / Type: Initial release
Revision 1.1	Oct 1, 2025	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9pdh.cif.gz	824.4 KB	Display	PDBx/mmCIF format
PDB format	pdb9pdh.ent.gz	569.3 KB	Display	PDB format
PDBx/mmJSON format	9pdh.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9pdh_validation.pdf.gz	2.1 MB	Display	wwPDB validaton report
Full document	9pdh_full_validation.pdf.gz	2.2 MB	Display
Data in XML	9pdh_validation.xml.gz	90.5 KB	Display
Data in CIF	9pdh_validation.cif.gz	116.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pd/9pdh ftp://data.pdbj.org/pub/pdb/validation_reports/pd/9pdh	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#265 - Jan 2022 Golgi Casein Kinase similarity (1)

Deposited unit

A: Adenosylhomocysteinase

B: Adenosylhomocysteinase

C: Adenosylhomocysteinase

D: Adenosylhomocysteinase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	89.315, 169.411, 127.368
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x,y+1/2,-z+1/2 #4: -x+1/2,-y,z+1/2

#1: Protein	Adenosylhomocysteinase / AdoHcyase / S-adenosyl-L-homocysteine hydrolase Mass: 47615.500 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Ahcy, Ahcy13, CG11654 / Production host: Escherichia coli (E. coli) / References: UniProt: Q27580, adenosylhomocysteinase
#2: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical	ChemComp-ADN / ADENOSINE Mass: 267.241 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₀H₁₃N₅O₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 844 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.53 Å³/Da / Density % sol: 51.38 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M Bis-Tris pH 6.5, 16% PEG MME 5000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5406 Å
Detector	Type: DECTRIS EIGER2 S 4M / Detector: PIXEL / Date: Apr 4, 2024 / Details: VariMax-VHP Arc Sec optics
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5406 Å / Relative weight: 1
Reflection	Resolution: 2.5→20.45 Å / Num. obs: 66928 / % possible obs: 99.25 % / Redundancy: 5.3 % / B_iso Wilson estimate: 24.56 Å² / CC_1/2: 0.925 / CC star: 0.98 / R_merge(I) obs: 0.2595 / R_pim(I) all: 0.1249 / R_rim(I) all: 0.2895 / Net I/σ(I): 6.51
Reflection shell	Resolution: 2.5→2.56 Å / Redundancy: 5.3 % / R_merge(I) obs: 0.8507 / Mean I/σ(I) obs: 1.93 / Num. unique obs: 4718 / CC_1/2: 0.459 / CC star: 0.793 / R_pim(I) all: 0.4134 / R_rim(I) all: 0.95 / % possible all: 99.94

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Processing

Software

Name	Version	Classification
PHENIX	1.21.2_5419	refinement
CrysalisPro		data reduction
CrysalisPro		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.5→20.45 Å / SU ML: 0.3542 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.1278
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2702	1996	2.98 %
R_work	0.2298	64892	-
obs	0.2311	66888	99.25 %

Solvent computation

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

Displacement parameters

B_iso mean: 31.65 Å²

Refinement step

Cycle: LAST / Resolution: 2.5→20.45 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13267	0	233	859	14359

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0042	13796
X-RAY DIFFRACTION	f_angle_d	0.7275	18738
X-RAY DIFFRACTION	f_chiral_restr	0.0464	2144
X-RAY DIFFRACTION	f_plane_restr	0.0079	2368
X-RAY DIFFRACTION	f_dihedral_angle_d	19.0877	5109

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 (%)
2.5-2.56	0.3354	141	0.292	4576	X-RAY DIFFRACTION	99.92
2.56-2.63	0.368	142	0.3019	4611	X-RAY DIFFRACTION	99.6
2.63-2.71	0.3517	142	0.2915	4625	X-RAY DIFFRACTION	99.75
2.71-2.8	0.3455	141	0.2838	4592	X-RAY DIFFRACTION	99.81
2.8-2.9	0.3191	142	0.2701	4639	X-RAY DIFFRACTION	99.94
2.9-3.01	0.2913	142	0.2668	4606	X-RAY DIFFRACTION	99.94
3.01-3.15	0.321	144	0.2563	4629	X-RAY DIFFRACTION	99.96
3.15-3.31	0.2526	143	0.2313	4667	X-RAY DIFFRACTION	100
3.31-3.52	0.2914	141	0.2282	4627	X-RAY DIFFRACTION	99.79
3.52-3.79	0.2932	142	0.2315	4639	X-RAY DIFFRACTION	99.31
3.79-4.17	0.251	143	0.2134	4658	X-RAY DIFFRACTION	99.36
4.17-4.76	0.2034	145	0.1787	4680	X-RAY DIFFRACTION	99.44
4.77-5.98	0.2025	145	0.1857	4692	X-RAY DIFFRACTION	98.37
5.98-20.45	0.203	143	0.1815	4651	X-RAY DIFFRACTION	94.61

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	1.36612791482	-0.189885686487	0.179579575921	0.544038483056	0.409175167216	1.24428024945	0.0724111123911	0.225488232018	0.249475011238	-0.0175706982152	-0.0734964775138	-0.100518849263	0.0178079693447	0.0517706295844	0.0653861446595	0.13735930328	0.0266808266095	0.00521373265967	0.215602227017	0.0832587900456	0.222247034494	32.2486616581	114.210594577	32.4992317188
2	0.720681652684	0.00929315243053	0.558803767571	0.441108934779	-0.19996368564	0.726754770942	-0.110345471056	0.0217759616391	0.707245887702	-0.177845158558	0.0358632816929	-0.155699869756	-0.421635530126	0.00897944205862	0.106349816039	0.346318252364	-0.00377089584763	-0.0599558593058	0.164234800619	0.0627523832977	0.450953686001	26.0263519934	130.395710769	34.5601783424
3	0.895223108712	0.170697337117	-0.523950220266	1.11756175296	0.168179983729	0.754731682857	-0.0773718181549	0.016032450106	0.248756803729	-0.0912118342102	0.0730128568206	-0.0210476731161	-0.011144639527	0.0412034619006	0.117511725925	0.146810398634	0.014616618349	-0.0320109398657	0.179619126185	-0.0224062946067	0.158214046529	13.2751139182	113.342140138	43.2296510723
4	1.37245867157	-0.267132146622	-0.316955468572	0.253374650153	-0.228388278495	1.11853269962	-0.0859569946585	-0.118903556275	0.145951600976	0.0987861896449	0.0341725389988	-0.0805500114736	-0.108348690001	-0.0779119604632	0.00697964050795	0.201846454996	0.0709705571698	-0.0303017503631	0.180213168046	-0.0328177759923	0.131267956264	6.03759282555	114.412162228	55.303808457
5	1.08773067613	-0.32883637096	-0.68381026053	0.877166421716	0.21600508414	1.31932721639	-0.0896332609058	-0.199711145452	0.296698035533	-0.0036551541404	-0.0521528505796	-0.164133518816	-0.461092621118	0.0467795219472	0.16016469449	0.188664715831	0.0312848675749	-0.0558167381177	0.187715301292	-0.0216054341144	0.217125408736	21.8593313307	116.615196614	59.0572811556
6	1.33960048353	0.1794073787	-0.353750043617	1.63092068864	0.798118201614	0.860451285944	0.0365620367574	0.599715858113	0.489788990931	-0.485926926108	-0.137443524349	-0.0459451514922	-0.0552406248231	-0.0947243470795	0.0662745269713	0.259007650587	0.06894293798	-0.0220362404585	0.309170928429	0.147089838252	0.215595801111	16.0362421978	116.564177299	23.9991305936
7	0.393144340389	-0.342390742229	0.48514520623	0.377226722269	-0.372445174378	0.667024378897	0.135730325588	0.286037694222	0.14541106348	-0.209361447102	-0.125094437679	0.0607520575381	0.129350280517	0.0404784294538	0.0676995058889	0.112685168424	0.21119638398	-0.175819649741	0.436723462661	0.213313250688	-0.00617289321086	-0.723696989277	108.947003771	18.8763215044
8	1.88095841165	-0.418791847384	-0.170588690692	1.20282755433	-0.028474460207	0.430601848936	0.021544270705	-0.373556077575	-0.0308309896664	0.13527611641	-0.0569135389936	-0.257537055888	0.0765152923694	0.260985799351	-0.0614109272078	0.263756291976	0.0790928211634	-0.0973493139373	0.270758062439	-0.00712167270483	0.179131123096	34.6980950738	96.9645440771	66.8585040396
9	1.28805104302	-0.104335017508	-0.249700020043	0.301879963745	-0.037723842823	0.401144751993	-0.0505782090925	-0.092473433142	-0.136325557394	0.0936159286225	0.0629744827416	-0.0721704110893	0.200206453954	0.258849706331	0.0193848697291	0.226680922348	0.0900593455676	-0.0313240515345	0.277297214681	0.00961667290354	0.135112728168	30.4462691421	84.9729209646	68.4498640343
10	2.14823932185	-1.0977655181	0.313211384185	1.34378502075	-0.348654168197	0.103158999704	0.290136835285	0.0450127592767	-0.408677636159	-0.28908510383	-0.100056552974	0.0592016569499	0.358434100009	0.233125495055	-0.118131742708	0.410600369869	0.0912756847963	-0.0318570450161	0.185800749351	0.0552357658076	0.250034999858	21.1233336584	72.4486290003	64.7851619314
11	0.169401457705	-0.156324854665	-0.144967053104	0.223826103062	0.115137679785	0.554811369366	0.089676924818	0.343499302056	-0.0109636537249	-0.0299513932645	0.129602000096	0.0359120604006	0.156367014111	0.00380858029039	-0.00437769787207	0.297373717497	0.0364005103571	-0.0539396243852	0.218350015551	-0.0656769437022	0.125329198278	12.2137128556	88.3835774241	42.4905057315
12	1.94682651951	0.0561521802923	-0.519907960094	1.67322640054	0.351628022105	0.941794775847	-0.172875831006	-0.285169316608	-0.379987118019	-0.231654039784	0.214387940793	-0.0155987366776	-0.172537395881	0.137201666047	0.113421437009	0.301346123147	0.115980309397	-0.0321529309859	0.232604275271	-0.0861789264645	0.151701186882	23.1922447382	81.3725105268	39.4116731642
13	0.744435970826	0.307708783481	-0.277340466918	0.514387517041	0.00738933018215	1.20690989361	-0.129861561716	0.0320648697452	-0.491432369599	-0.0434445787563	-0.0200254336721	-0.34335439003	-0.208651129367	0.356621526618	-0.0129244695315	0.188276569917	0.202340082448	-0.154089257296	0.262757767613	0.0856618311831	0.0272852455692	26.8250686971	87.4737946605	49.2963707699
14	1.39754481106	-0.0666536824461	0.285584322017	0.264284325023	0.341398910721	0.860282935433	-0.139502255371	-0.296003876864	-0.188117069666	0.13479182326	0.123087977459	0.0932752599817	0.146291963078	-0.305313871061	0.0318456380869	0.297298970148	0.0139935415823	0.0393051560056	0.312959608493	0.103820092748	0.214640739864	1.81365194473	83.8545997682	71.8233313858
15	1.66348699273	-0.192944276274	0.21812121979	0.930584546095	-0.172569426574	0.523521019604	-0.0328101717904	0.221743595643	0.0593074449267	-0.110027885261	0.138554066338	0.126880217473	-0.00697232281789	-0.0423412879417	-0.0761091306914	0.16763559267	-0.00721582638839	-0.012923158611	0.305765414317	0.0168282249903	0.188946507961	-31.1784627171	115.060285042	33.0681661635
16	1.2601307196	-0.502343868769	0.0411167261918	0.898798103022	-0.527784642694	0.41402530713	-0.0663291972426	0.332719828755	0.150062460788	-0.0935514709621	-0.0831919103222	-0.0503433281844	-0.120927297963	0.0109711366129	0.0134518222793	0.253079828795	-0.0292223726086	-0.0443267261803	0.268906018222	0.00649920677516	0.191952293968	-15.9108911079	115.206516709	27.4949611814
17	1.46372770014	0.566124135594	0.290173797632	1.50553353752	0.00482054741345	1.49030140707	0.0862134584862	0.383833989017	-0.114698417243	-0.244296417995	-0.0591493951477	0.209099604511	0.117980779658	-0.153949939023	-0.0259944597115	0.204429471793	0.063864362964	-0.0695936533237	0.30307156864	-0.0734330331343	0.188710793131	-7.60549601503	94.0842464764	26.4153290674
18	0.802450360796	0.193311297526	-0.0809960339072	0.886505503672	-0.0543686877757	0.474679056026	-0.0656965623293	0.100122287863	0.127841048694	-0.030386822809	0.0519786551547	0.116755119674	-0.0925805591514	-0.0486082292208	0.0340432945923	0.184201602966	0.0541283271345	-0.0382394806801	0.205798957496	-0.00960855507871	0.248157539789	-11.8055962081	115.733485798	37.2579423027
19	1.94623168697	0.629371616209	-1.29600372275	0.688080002205	-0.747373295137	1.12881441605	-0.0312615570165	-0.0447710423744	-0.0891655532635	0.061450520769	0.187835498724	0.427230257662	0.0711791777392	-0.238686158162	0.123095563041	0.228296836306	-0.0431929544329	-0.0927576118214	0.52544981346	-0.117398600565	0.529253310738	-29.0834600867	76.2547076054	38.2500208858
20	0.637935842919	0.0474443489869	-0.235420685791	1.15623815481	0.291282398933	0.746190318158	-0.184109790521	-0.186519730551	-0.315809510025	0.287968903465	0.170860983047	0.0880928089416	0.103016125758	-0.157942282354	0.0388771874253	0.357018165332	0.0563786423791	-0.00301629938782	0.370612542067	-0.0178131453155	0.460108691589	-21.1840688536	71.350644962	52.8427354006
21	2.40938499031	-1.27252475669	1.04737990405	1.10803176249	-0.429441182571	0.919818990038	-0.00768218980004	-0.279987604998	-0.0619670594686	0.147225271112	0.0818812199685	0.161149252936	-0.0331413582582	-0.121614408269	-0.0883739637013	0.189479373898	-0.00353394375	0.0360243795115	0.211523484648	-0.0191747352285	0.138926962022	-16.1191180692	98.3372931194	60.7205796621
22	1.67311998372	-0.160042090811	-0.248667589383	0.79048977165	-0.167347360565	0.607422419628	-0.0273405245047	-0.149176569733	-0.555552139915	-0.113582380025	-0.0602025793678	0.205841977973	0.336363046599	0.0310446952954	0.0523152989986	0.326002283105	0.00864894654014	-0.0287936289009	0.194743552518	-0.0190640290114	0.384645428947	-3.01117101904	70.6221147511	48.4154917442

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 2 through 105 )	A	A	2 - 105	1 - 104
2	2	chain 'A' and (resid 106 through 169 )	A	A	106 - 169	105 - 168
3	3	chain 'A' and (resid 170 through 222 )	A	A	170 - 222	169 - 221
4	4	chain 'A' and (resid 223 through 298 )	A	A	223 - 298	222 - 297
5	5	chain 'A' and (resid 299 through 354 )	A	A	299 - 354	298 - 353
6	6	chain 'A' and (resid 355 through 402 )	A	A	355 - 402	354 - 401
7	7	chain 'A' and (resid 403 through 432 )	A	A	403 - 432	402 - 431
8	8	chain 'B' and (resid 1 through 27 )	B	D	1 - 27	1 - 27
9	9	chain 'B' and (resid 28 through 141 )	B	D	28 - 141	28 - 141
10	10	chain 'B' and (resid 142 through 189 )	B	D	142 - 189	142 - 189
11	11	chain 'B' and (resid 190 through 274 )	B	D	190 - 274	190 - 274
12	12	chain 'B' and (resid 275 through 307 )	B	D	275 - 307	275 - 307
13	13	chain 'B' and (resid 308 through 374 )	B	D	308 - 374	308 - 374
14	14	chain 'B' and (resid 375 through 432 )	B	D	375 - 432	375 - 432
15	15	chain 'C' and (resid 0 through 142 )	C	G	0 - 142	1 - 143
16	16	chain 'C' and (resid 143 through 207 )	C	G	143 - 207	144 - 208
17	17	chain 'C' and (resid 208 through 322 )	C	G	208 - 322	209 - 323
18	18	chain 'C' and (resid 323 through 432 )	C	G	323 - 432	324 - 433
19	19	chain 'D' and (resid 3 through 27 )	D	J	3 - 27	1 - 25
20	20	chain 'D' and (resid 28 through 207 )	D	J	28 - 207	26 - 205
21	21	chain 'D' and (resid 208 through 342 )	D	J	208 - 342	206 - 340
22	22	chain 'D' and (resid 343 through 432 )	D	J	343 - 432	341 - 430

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