PDB-9nth: Helix pomatia AMP deaminase (HPAMPD) in complex with Pentostatin ...

ID or keywords:

Entry

Database: PDB / ID: 9nth

Title

Helix pomatia AMP deaminase (HPAMPD) in complex with Pentostatin monophosphate (PMP)

Components

AMP Deaminase

Keywords

HYDROLASE / Helix pomatia AMP deaminase (HPAMPD) / adenosine deaminase 2 (ADA2) / ADENOSINE 5'-MONOPHOSPHATE DEAMINASE / Deoxycoformycin

Function / homology

: / DI(HYDROXYETHYL)ETHER

Function and homology information

Biological species

Helix pomatia (Roman snail)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.61 Å

Authors

Kaur, G. / Horton, J.R. / Cheng, X.

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	R35GM134744	United States
Cancer Prevention and Research Institute of Texas (CPRIT)	RR160029	United States

Citation

Journal: To Be Published
Title: Structural basis of substrate specificity of Helix pomatia AMP deaminase and a chimeric ADGF adenosine deaminase
Authors: Kaur, G. / Horton, J.R. / Tzertzinis, G. / Schildkraut, I. / Cheng, X.

History

Deposition	Mar 18, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 18, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9nth.cif.gz	1 MB	Display	PDBx/mmCIF format
PDB format	pdb9nth.ent.gz		Display	PDB format
PDBx/mmJSON format	9nth.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nt/9nth ftp://data.pdbj.org/pub/pdb/validation_reports/nt/9nth	HTTPS FTP

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Related structure data

Related structure data	9nteC 9ntfC 9ntkC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: AMP Deaminase

B: AMP Deaminase

C: AMP Deaminase

D: AMP Deaminase

hetero molecules

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

1

A: AMP Deaminase

D: AMP Deaminase

hetero molecules

defined by author&software
129 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: AMP Deaminase

C: AMP Deaminase

hetero molecules

defined by author&software
130 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	75.992, 81.936, 212.195
Angle α, β, γ (deg.)	90.000, 92.134, 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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Protein , 1 types, 4 molecules ABCD

#1: Protein	AMP Deaminase Mass: 61251.590 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helix pomatia (Roman snail) / Production host: Komagataella pastoris (fungus)

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Sugars , 2 types, 15 molecules

#2: Polysaccharide

2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source

Descriptor	Type	Program
DGlcpNAcb1-4DGlcpNAcb1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1	WURCS	PDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}	LINUCS	PDB-CARE

#4: Sugar

ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE

Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 11
Source method: isolated from a genetically manipulated source
Formula: C₈H₁₅NO₆

Identifier	Type	Program
DGlcpNAcb	CONDENSED IUPAC CARBOHYDRATE SYMBOL	GMML 1.0
N-acetyl-b-D-glucopyranosamine	COMMON NAME	GMML 1.0
b-D-GlcpNAc	IUPAC CARBOHYDRATE SYMBOL	PDB-CARE 1.0
GlcNAc	SNFG CARBOHYDRATE SYMBOL	GMML 1.0

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Non-polymers , 7 types, 2425 molecules

#3: Chemical	... ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 101 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Chemical	ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER Mass: 209.240 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₁₉NO₅ / Comment: pH buffer*YM
#6: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₃H₈O₃
#7: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#8: Chemical	ChemComp-A1CDW / pentostatin 5'-phosphate / (8S)-3-(2-deoxy-5-O-phosphono-beta-D-threo-pentofuranosyl)-3,6,7,8-tetrahydroimidazo[4,5-d][1,3]diazepin-8-ol / 2'-deoxycoformycin 5'-phosphate Mass: 348.249 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₁H₁₇N₄O₇P / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#10: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 2305 / 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: 2.69 Å³/Da / Density % sol: 54.35 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1 M BIS-TRIS pH 6.5, 20% w/v Polyethylene glycol monomethyl ether 5,000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.92 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 7, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.92 Å / Relative weight: 1
Reflection	Resolution: 1.61→42.73 Å / Num. obs: 332916 / % possible obs: 100 % / Redundancy: 3.9 % / B_iso Wilson estimate: 24.55 Å² / CC_1/2: 0.995 / R_pim(I) all: 0.084 / Net I/σ(I): 5.7
Reflection shell	Resolution: 1.61→1.64 Å / Num. unique obs: 16484 / CC_1/2: 0.334 / R_pim(I) all: 0.647

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Processing

Software

Name	Version	Classification
PHENIX	1.21.2_5419	refinement
XDS		data reduction
autoPROC		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.61→42.73 Å / SU ML: 0.2038 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.8719
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1987	16268	4.9 %
R_work	0.1666	315661	-
obs	0.1681	331929	98.94 %

Solvent computation

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

Displacement parameters

B_iso mean: 25.85 Å²

Refinement step

Cycle: LAST / Resolution: 1.61→42.73 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	16052	0	849	2305	19206

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0152	17331
X-RAY DIFFRACTION	f_angle_d	1.3212	23368
X-RAY DIFFRACTION	f_chiral_restr	0.0826	2604
X-RAY DIFFRACTION	f_plane_restr	0.0131	2945
X-RAY DIFFRACTION	f_dihedral_angle_d	14.0196	6778

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 (%)
1.61-1.63	0.3361	584	0.3351	10103	X-RAY DIFFRACTION	96.04
1.63-1.65	0.3319	562	0.321	10262	X-RAY DIFFRACTION	96.95
1.65-1.67	0.3344	529	0.3116	10323	X-RAY DIFFRACTION	97.6
1.67-1.69	0.3153	594	0.2951	10353	X-RAY DIFFRACTION	98.12
1.69-1.71	0.3276	592	0.2914	10279	X-RAY DIFFRACTION	98.12
1.71-1.74	0.3002	549	0.2755	10416	X-RAY DIFFRACTION	98.32
1.74-1.76	0.2988	546	0.2668	10381	X-RAY DIFFRACTION	98.49
1.76-1.79	0.2861	511	0.2579	10479	X-RAY DIFFRACTION	98.72
1.79-1.81	0.2803	544	0.2487	10530	X-RAY DIFFRACTION	98.95
1.81-1.84	0.2793	544	0.2305	10469	X-RAY DIFFRACTION	99.02
1.84-1.88	0.2492	527	0.2189	10530	X-RAY DIFFRACTION	99.01
1.88-1.91	0.2424	515	0.2085	10538	X-RAY DIFFRACTION	99.06
1.91-1.95	0.246	542	0.2052	10533	X-RAY DIFFRACTION	99.13
1.95-1.99	0.2389	492	0.1924	10569	X-RAY DIFFRACTION	99.26
1.99-2.03	0.2254	498	0.1773	10594	X-RAY DIFFRACTION	99.29
2.03-2.08	0.2145	529	0.1655	10507	X-RAY DIFFRACTION	99.28
2.08-2.13	0.2072	513	0.1645	10560	X-RAY DIFFRACTION	99.4
2.13-2.19	0.1922	546	0.1567	10585	X-RAY DIFFRACTION	99.39
2.19-2.25	0.1934	553	0.152	10547	X-RAY DIFFRACTION	99.39
2.25-2.32	0.1902	564	0.15	10566	X-RAY DIFFRACTION	99.52
2.32-2.41	0.1846	589	0.1487	10516	X-RAY DIFFRACTION	99.55
2.41-2.5	0.1961	587	0.1499	10552	X-RAY DIFFRACTION	99.51
2.5-2.62	0.1802	543	0.1462	10619	X-RAY DIFFRACTION	99.52
2.62-2.75	0.1881	506	0.1482	10589	X-RAY DIFFRACTION	99.44
2.75-2.93	0.193	542	0.1532	10704	X-RAY DIFFRACTION	99.57
2.93-3.15	0.1816	493	0.1532	10584	X-RAY DIFFRACTION	99.1
3.15-3.47	0.1776	546	0.1503	10626	X-RAY DIFFRACTION	99.29
3.47-3.97	0.1485	519	0.1322	10654	X-RAY DIFFRACTION	99.38
3.97-5	0.1348	499	0.1168	10806	X-RAY DIFFRACTION	99.98
5-42.73	0.1757	610	0.1516	10887	X-RAY DIFFRACTION	99.63

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	0.309162361298	-0.0790948444233	-0.141796062581	0.514244612568	0.355569871681	0.971162275288	-0.026806023189	-0.0462108001183	-0.0372719334349	0.0255977680471	-0.0209204774141	0.116315553801	-0.0124387890789	-0.146918467673	0.0458797160934	0.126841630173	-0.00028512618618	0.00966884747845	0.182917002597	0.0194051558212	0.189805256916	-40.9217694806	-8.43715509948	21.53941382
2	1.15819323425	-0.815333005594	0.719982328032	5.21535305424	-0.377827734435	1.6464414054	0.0980610720631	0.0706322406218	-0.362232910022	0.116864521358	0.00288919059494	-0.0611843960438	0.264771962488	0.150964487072	-0.111993480362	0.12630889091	0.00744372462559	-0.0137431663853	0.145219923963	-0.0261658774584	0.228892815039	-15.2086196945	-39.0764691063	4.44029288883
3	0.716438031707	-0.27524451588	-0.13407800895	0.586046102846	0.0460290810043	1.35922654909	0.0311891115259	0.120967701255	-0.139660341714	-0.0104657363086	-0.0207951140596	0.0302725213455	0.0625950217032	-0.00301915466568	-0.0111323575147	0.132585263358	-0.0158919107744	0.00378520978626	0.126683007637	-0.0183793104395	0.192060661405	-20.8235855521	-26.3231283942	-1.19630990108
4	1.09663015076	-0.0882239773879	-0.0642960163539	0.399984146994	0.184922781181	0.781473709096	0.0108127964279	0.140472929711	0.00480063697971	-0.0600456036981	-0.0119712856039	0.0122872728256	-0.0607631986982	-0.0149963755918	-0.00251021158484	0.143308934499	0.00222299826499	-0.00342869202295	0.120140931153	0.0123757023949	0.152398670286	-24.7992632706	-9.60647214901	2.88330951958
5	0.184456717072	0.0898258978963	-0.00299775218672	0.92467717666	-0.603072075437	0.810445495377	0.0128710052882	0.027850273121	-0.0198426521944	-0.0459841863295	-0.0180714067473	-0.0941003774682	0.0593372220049	0.0515587199484	0.0106295778859	0.174811563566	0.00618257297391	0.00198070812326	0.247615800755	-0.00829295180422	0.182494022872	37.4804972522	-21.6531923441	86.1514293576
6	3.27804654442	-1.00069241985	0.541184710821	5.83565155425	0.477374453009	3.92655495496	0.0510929772453	-0.103286150279	-0.3638869647	-0.331471406628	0.185014351022	0.612545296869	0.478215285255	-0.551580411825	-0.193001448215	0.360460379374	-0.150102150637	-0.136730377845	0.297914795135	0.0880558560963	0.270912753896	12.6897060307	-52.7188487646	89.9373086526
7	0.3979562038	-0.037305430601	0.148729761442	0.738873863031	-0.294775633762	0.42458194871	0.0357007528793	-0.151654173407	-0.0487059475558	0.110718519367	0.0124226234458	0.0750232727203	0.0461112173739	-0.145895940194	-0.0474734083276	0.181190359175	-0.0327618652224	-0.00875990265772	0.251587391691	0.013931775407	0.13890210131	20.6078570872	-27.2143379641	101.073989017
8	2.51455075522	-1.87554453177	-1.25376295435	3.27239385554	1.65939554149	7.03570834093	-0.0275479884094	-0.279601757454	0.0455741892931	0.137680456335	-0.0117855162562	-0.244089068423	0.116844815419	0.243790359613	-0.0110296642966	0.13490811166	-0.0583937776539	-0.0499831107583	0.166750724971	0.0223319672162	0.185096041319	44.2606237381	-24.0416262165	100.07613488
9	2.26496299184	-0.76483394132	0.565321860105	4.2462309786	-1.93581612919	2.82561089035	-0.175737563391	-0.34676964697	-0.155345380714	0.913989124831	0.139451046846	0.192021171391	-0.463551379395	-0.313000643797	0.0398733411266	0.325926749925	0.0500379853838	0.0509201278834	0.335054928885	-0.062462787014	0.199276234181	8.94572932958	-1.02920315414	102.801746276
10	1.29026712148	-0.268111934975	-0.153293728177	2.52944373249	-0.19446087713	0.771381496447	-0.00605561072097	-0.211085566545	-0.0691451318058	0.158639566887	0.0445927021592	0.334448232583	0.00551668713891	-0.260330518268	-0.0400762328428	0.130289602402	-0.0014462001464	0.00185256118234	0.297169509757	0.00397890979757	0.171972313102	1.08365272333	-7.3189312507	80.7251008097
11	1.54083634417	1.13346588969	2.00900789685	2.53280256081	1.30260255333	3.13180818254	0.00362898946087	0.268699251854	-0.013503986068	-0.178547568956	0.0363650117047	-0.0752074377758	0.118011140597	0.159550993029	-0.0270737329436	0.115479583979	0.0154496943704	0.012494081509	0.195473439954	0.0190902488481	0.126018216519	13.553035066	-8.58311602766	46.451839663
12	0.54720113926	0.385773447007	-0.0733839382191	0.63219878899	-0.114060810502	0.741172058923	0.00610608260062	0.0497591204464	0.0724799894098	-0.0361837852761	0.0188017997538	0.0371991865223	-0.0685090634021	-0.0455965964369	-0.0278568717378	0.161390913511	0.0147777755025	-0.00577232463952	0.193678948357	0.006855798917	0.166753559269	19.9074701738	4.09950813516	58.0621342901
13	0.790152628345	0.0229470447713	-0.284149323116	0.49842346857	-0.250869158901	1.05655644832	0.025609185275	-0.094176754115	0.0798892788636	0.0570479301336	-0.0192295287163	-0.00466188826999	-0.099832091124	0.00864333005466	-0.00679622825568	0.155519396389	0.0035056012559	-0.00622258808136	0.171615830601	-0.0157416615877	0.160104074693	25.0429671332	0.0873914220975	75.2236768097
14	3.30779415794	1.76897142505	-0.377387033154	3.30710984088	-0.882632181321	1.65770324544	0.113482366997	-0.0725187403969	0.32247801288	0.170983854769	-0.0265448320164	0.364907294743	-0.259684559793	-0.359594244251	-0.106235338209	0.191859456894	0.0692664080867	0.0238633486476	0.243887397761	-0.0496111017907	0.168394012463	3.68211472468	10.8685935621	79.2600806033
15	0.65586538334	0.194092608965	0.223278806531	0.954019633825	0.355610818424	0.936011868631	-0.0218087483256	0.134533649866	0.075037664666	-0.162454442331	0.0425762818765	-0.0714929189007	-0.127405885079	0.136708016802	-0.0267091873371	0.146566234265	-0.0217122699135	0.018720172448	0.186139310738	0.0245865391414	0.20280274614	-4.01635038557	3.68061522818	19.1763626617
16	1.33370678747	-1.4631952613	1.53809854177	3.05427765484	-1.2758883165	2.33432944472	-0.00599344508749	-0.281966004693	-0.0795420255988	0.167818247904	0.0614300164839	0.0703006351494	0.166679192686	-0.148980503398	-0.0404764936575	0.122695034301	-0.0246393054225	0.0112473992521	0.209691576299	0.020853927608	0.125140714342	-13.6410318503	-10.0642844809	58.9254548991
17	0.539526823776	-0.0426375633289	-0.0985378342474	0.233356010878	0.0332457592371	0.65061941904	0.0203542739963	-0.0674883308422	0.075316716901	0.0245234733014	-0.0043234202499	-0.0105566635303	-0.0837726825965	0.0151306612417	-0.0179717591237	0.147582444463	-0.0123432229262	-0.00325083094072	0.137015490269	0.00247137918577	0.16895833805	-22.0270852714	5.89116655784	40.903813223
18	7.21455321107	-3.0480309233	-5.14529024765	1.44615212518	2.30097589987	4.43100044419	0.367978819125	-0.416486827275	0.543971116585	-0.239516814462	0.0292672217722	-0.277827358847	-0.371491012474	0.467824302703	-0.39365460905	0.189099356105	-0.0741847053234	0.00543879150342	0.212484809504	0.0248398732279	0.238682033719	6.54847877637	15.3251772815	29.5645910989

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 'C' and (resid 30 through 119 )	C	C	30 - 119	30 - 119
2	2	chain 'C' and (resid 120 through 194 )	C	C	120 - 194	120 - 194
3	3	chain 'C' and (resid 195 through 287 )	C	C	195 - 287	195 - 287
4	4	chain 'C' and (resid 288 through 525 )	C	C	288 - 525	288 - 525
5	5	chain 'D' and (resid 30 through 142 )	D	D	30 - 142	30
6	6	chain 'D' and (resid 143 through 194 )	D	D	143 - 194	143 - 194
7	7	chain 'D' and (resid 195 through 478 )	D	D	195 - 478	195 - 478
8	8	chain 'D' and (resid 479 through 526 )	D	D	479 - 526	479 - 526
9	9	chain 'A' and (resid 31 through 61 )	A	A	31 - 61	31 - 61
10	10	chain 'A' and (resid 62 through 119 )	A	A	62 - 119	62 - 119
11	11	chain 'A' and (resid 120 through 194 )	A	A	120 - 194	120 - 194
12	12	chain 'A' and (resid 195 through 322 )	A	A	195 - 322	195 - 322
13	13	chain 'A' and (resid 323 through 478 )	A	A	323 - 478	323 - 478
14	14	chain 'A' and (resid 479 through 527 )	A	A	479 - 527	479 - 527
15	15	chain 'B' and (resid 31 through 119 )	B	B	31 - 119	31 - 119
16	16	chain 'B' and (resid 120 through 194 )	B	B	120 - 194	120 - 194
17	17	chain 'B' and (resid 195 through 496 )	B	B	195 - 496	195 - 496
18	18	chain 'B' and (resid 497 through 535 )	B	B	497 - 535	497 - 535

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