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

ID or keywords:

Entry

Database: PDB / ID: 9ntg

Title

Helix pomatia AMP deaminase (HPAMPD) in complex with Pentostatin

Components

Helix pomatia AMP deaminase

Keywords

HYDROLASE / Helix pomatia AMP deaminase (HPAMPD) / Pentostatin / Deoxycoformycin / Adenosine 5'-monophosphate deaminase

Function / homology

2'-DEOXYCOFORMYCIN

Function and homology information

Biological species

Helix pomatia (Roman snail)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.63 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: Helix pomatia AMP deaminase (HPAMPD) in complex with Pentostatin (DCF)
Authors: Kaur, G. / Horton, J.R. / 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	9ntg.cif.gz	1 MB	Display	PDBx/mmCIF format
PDB format	pdb9ntg.ent.gz	698.4 KB	Display	PDB format
PDBx/mmJSON format	9ntg.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9ntg_validation.pdf.gz	1.9 MB	Display	wwPDB validaton report
Full document	9ntg_full_validation.pdf.gz	1.9 MB	Display
Data in XML	9ntg_validation.xml.gz	107.7 KB	Display
Data in CIF	9ntg_validation.cif.gz	151.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nt/9ntg ftp://data.pdbj.org/pub/pdb/validation_reports/nt/9ntg	HTTPS FTP

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Related structure data

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: Helix pomatia AMP deaminase

B: Helix pomatia AMP deaminase

C: Helix pomatia AMP deaminase

D: Helix pomatia AMP deaminase

hetero molecules

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

1

A: Helix pomatia AMP deaminase

D: Helix pomatia AMP deaminase

hetero molecules

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

2

B: Helix pomatia AMP deaminase

C: Helix pomatia AMP deaminase

hetero molecules

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

Unit cell

Length a, b, c (Å)	76.128, 81.983, 212.016
Angle α, β, γ (deg.)	90.000, 92.265, 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	Helix pomatia 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, 16 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.: 1
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

#3: 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.: 15 / Source method: obtained synthetically / 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 , 5 types, 2218 molecules

#4: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Formula: Zn
#5: Chemical	... ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 51 / Source method: obtained synthetically / Formula: C₂H₆O₂
#6: 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
#7: Chemical	ChemComp-DCF / 2'-DEOXYCOFORMYCIN Mass: 268.269 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₁H₁₆N₄O₄ / Feature type: SUBJECT OF INVESTIGATION
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 2157 / 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: 2.7 Å³/Da / Density % sol: 54.41 %
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: Jun 1, 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: 1.63→20 Å / Num. obs: 313765 / % possible obs: 96.9 % / Redundancy: 4.4 % / B_iso Wilson estimate: 21.85 Å² / CC_1/2: 0.997 / R_pim(I) all: 0.063 / Net I/σ(I): 7.3
Reflection shell	Resolution: 1.63→1.66 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 14025 / CC_1/2: 0.483 / R_pim(I) all: 0.617

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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: 1.63→20 Å / SU ML: 0.1591 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.1606
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1821	15742	5.02 %
R_work	0.1563	297944	-
obs	0.1576	313686	96.73 %

Solvent computation

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

Displacement parameters

B_iso mean: 23.3 Å²

Refinement step

Cycle: LAST / Resolution: 1.63→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	16059	0	550	2157	18766

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0082	17138
X-RAY DIFFRACTION	f_angle_d	0.9438	23223
X-RAY DIFFRACTION	f_chiral_restr	0.0608	2597
X-RAY DIFFRACTION	f_plane_restr	0.0099	2955
X-RAY DIFFRACTION	f_dihedral_angle_d	13.0248	6697

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 (%)
1.63-1.65	0.3211	493	0.2857	8854	X-RAY DIFFRACTION	86.76
1.65-1.67	0.2824	522	0.271	9114	X-RAY DIFFRACTION	89.71
1.67-1.69	0.2778	484	0.2588	9289	X-RAY DIFFRACTION	90.83
1.69-1.71	0.2739	478	0.2503	9560	X-RAY DIFFRACTION	92.86
1.71-1.73	0.2559	510	0.2327	9518	X-RAY DIFFRACTION	93.61
1.73-1.76	0.2529	484	0.2275	9873	X-RAY DIFFRACTION	96.15
1.76-1.78	0.2533	481	0.2154	9962	X-RAY DIFFRACTION	96.88
1.78-1.81	0.2389	506	0.2092	9937	X-RAY DIFFRACTION	96.66
1.81-1.84	0.2241	537	0.1958	9902	X-RAY DIFFRACTION	97.51
1.84-1.87	0.2288	522	0.1874	9985	X-RAY DIFFRACTION	96.83
1.87-1.9	0.2075	515	0.1868	9921	X-RAY DIFFRACTION	97.13
1.9-1.93	0.2136	524	0.1862	9943	X-RAY DIFFRACTION	97.71
1.93-1.97	0.2133	460	0.1817	10065	X-RAY DIFFRACTION	97.27
1.97-2.01	0.2154	509	0.174	10002	X-RAY DIFFRACTION	97.27
2.01-2.05	0.1967	538	0.162	9978	X-RAY DIFFRACTION	97.66
2.05-2.1	0.1831	573	0.1602	10006	X-RAY DIFFRACTION	98.04
2.1-2.15	0.1787	573	0.1544	9988	X-RAY DIFFRACTION	97.9
2.15-2.21	0.1941	533	0.1561	10015	X-RAY DIFFRACTION	97.94
2.21-2.28	0.1903	510	0.1579	10109	X-RAY DIFFRACTION	98.03
2.28-2.35	0.1844	571	0.152	9993	X-RAY DIFFRACTION	98.14
2.35-2.43	0.1776	531	0.1495	10097	X-RAY DIFFRACTION	98.24
2.43-2.53	0.1864	550	0.1538	10087	X-RAY DIFFRACTION	98.23
2.53-2.65	0.1862	505	0.1464	10159	X-RAY DIFFRACTION	98.51
2.65-2.79	0.1824	520	0.1496	10133	X-RAY DIFFRACTION	98.66
2.79-2.96	0.1731	537	0.1463	10158	X-RAY DIFFRACTION	98.58
2.96-3.19	0.1772	563	0.1474	10156	X-RAY DIFFRACTION	98.79
3.19-3.51	0.1679	574	0.1414	10163	X-RAY DIFFRACTION	98.77
3.51-4.01	0.1482	596	0.127	10189	X-RAY DIFFRACTION	98.83
4.01-5.04	0.1328	579	0.1125	10232	X-RAY DIFFRACTION	98.93
5.04-20	0.1481	464	0.1427	10556	X-RAY DIFFRACTION	99.19

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	0.768516702341	0.126831513264	0.572565795194	3.17925638494	0.838197561909	1.88795317384	0.0522278957759	-0.0361634367898	-0.181472395022	-0.274147288716	0.113821326112	0.319743054366	0.374461318909	-0.303265379769	-0.148227875555	0.323620253833	-0.0978425182838	-0.0877895681212	0.244834786026	0.075388130971	0.191628999817	15.8050720044	-50.1177154532	92.1831388001
2	0.315779901355	-0.0701100302392	0.160493650983	0.555545785216	-0.245831425768	0.375587530547	0.0354585453007	-0.106267562191	-0.0333836863504	0.0807465066951	0.016490476726	0.0507354114396	0.0471930837974	-0.116826878735	-0.0519730045415	0.201201652319	-0.0299365887356	-0.00373931795605	0.217163035844	0.0115733885787	0.123381026053	20.4609961712	-27.2742090389	100.985565279
3	3.04153609669	-1.27497350119	-1.10182340906	2.59025504695	0.985180076168	4.71911596206	0.0296458934672	-0.236207821569	-0.0130634851773	0.131679058445	-0.0310268929509	-0.182908993775	0.0985746941857	0.138002736015	-0.0226863614132	0.128514102363	-0.0399449777577	-0.0469767238427	0.110878625298	0.0101850134474	0.128833742842	44.0854688567	-24.1065147926	100.000831754
4	0.376048644652	-0.239500796542	0.0784700710336	0.888211260814	-0.0316972670947	0.87259855498	-0.0242507117596	-0.200392635099	0.00250551062602	0.188561124075	0.0499748471853	0.154571972469	-0.0129482046188	-0.194953163051	-0.0289105719824	0.151207608968	0.00481092632699	0.0399749321145	0.26659199104	0.000483161608642	0.145882172956	3.65106566968	-5.20435629172	88.2862481848
5	1.38905896366	0.668113580917	1.407857307	2.02564282481	0.965832728754	2.38140194704	0.00130155486298	0.227730578909	-0.027161170713	-0.135678133655	0.00259259185619	0.0102881556245	0.136911133702	0.0996622292464	0.000501072056272	0.122053671899	0.0125438790793	0.0102855837343	0.189894698055	0.0198410494843	0.112064576877	13.3502672276	-8.5098597739	46.5515425646
6	0.427862404182	0.0412473717485	0.0113150948033	0.344898982646	-0.101817862408	0.527581110041	0.015671745435	0.00107667438893	0.0534708845891	0.0122161409776	0.0033149579012	0.0102245837923	-0.0454713384869	-0.0304154246878	-0.018788795707	0.158343087502	0.00885984620349	0.00427152243244	0.166038755348	-0.00232155140432	0.143490950467	21.7048128651	2.43167561901	67.7889576799
7	7.95444725882	4.67364563435	-1.74400268082	5.67038674516	-1.70421013807	1.6638382664	0.216526688176	-0.108980049418	0.380156295035	0.263769424343	-0.0401414341053	0.520140016266	-0.247648048458	-0.329700043409	-0.229052345259	0.195275188235	0.0792830522597	0.0322617341697	0.28496362246	-0.0240378823888	0.165269182306	-1.34505472676	11.3042405087	78.8354766674
8	0.464922271773	0.218138674296	0.0654819904262	0.826039371352	0.102955901663	0.903378800088	-0.0138896403379	0.0941235522355	0.0672878653433	-0.144152272808	0.0458763315964	-0.0433203126919	-0.0952789538159	0.0885723418311	-0.0285032303788	0.128127544503	-0.0166317024977	0.0234564195882	0.144828755569	0.0194127636397	0.148411466961	-4.26076497418	3.79598792211	18.8333528667
9	1.16611588933	-0.89122610254	1.0903508592	2.3955767601	-1.01071145612	2.10402938214	0.00479018080943	-0.229587083723	-0.0960121677595	0.144845266797	0.0375914572322	0.0457940384531	0.18335547094	-0.128194207708	-0.0319608435363	0.12719044818	-0.0188120303279	0.0122030205019	0.180491709069	0.0142340858697	0.105755620095	-13.8408126803	-10.1101155946	58.8622836869
10	0.44673183395	-0.030234043613	-0.0551586552642	0.236328847039	0.0546822691554	0.491498102185	0.0128264449467	-0.0639547308107	0.0509192551339	0.0180429588091	-6.45246474164E-5	0.000217362744176	-0.0602176006982	0.00648218827018	-0.0125750362368	0.14431329955	-0.0066310734585	0.00210645022233	0.129957523783	0.00307361046222	0.140563884405	-22.198878674	5.81398295501	40.907225825
11	5.18377590411	-1.70655818965	-3.62361575531	0.815701101761	1.26062530074	3.24749780085	0.278786570892	-0.187589168346	0.342912233449	-0.161624888559	-0.0295385395298	-0.172440102547	-0.294826549716	0.338848874203	-0.304984934736	0.191310496438	-0.0588981155282	-0.000558568639867	0.213465171023	0.0166072631041	0.200964084241	6.46935702958	15.3260576985	29.5451978625
12	0.258100447202	-0.0860574115852	-0.114326470208	0.488065581921	0.247465612389	0.816576118179	-0.0186324753295	-0.0300655152161	-0.027129819866	0.0340604072647	-0.0158220895508	0.0740843041699	-0.00781742393345	-0.118386477699	0.034542936401	0.123479272041	-0.00346560750672	0.013578450742	0.159387677572	0.0159060600466	0.16400406201	-41.1733187499	-8.34386188229	21.25083046
13	0.780227291675	-0.822166442836	0.460905880872	4.19866591375	-0.159215792008	1.32359909637	0.0297390063992	0.0226493882563	-0.272086474596	0.165313609379	0.0506853704345	0.0224835496771	0.187069226707	0.103381998292	-0.0965591769353	0.115056612941	0.000297099553136	0.00167261210256	0.128547623597	-0.0166942896732	0.197002750002	-15.1422065907	-38.948894748	4.32726727469
14	0.596641482524	-0.203804729928	-0.161639131498	0.588262931927	0.0287119141705	0.96323017738	0.0150532994945	0.0828972324333	-0.101218526153	-0.00627224850257	-0.0196529345806	0.0263357690757	0.0320819875502	0.0124775983063	0.00671267553048	0.121830633455	-0.0120448395696	0.00796071984088	0.108950975507	-0.012082964124	0.155100253687	-20.9195566854	-26.3596931938	-1.32455634964
15	0.761288959863	-0.0774327276518	-0.051180187794	0.443738288119	0.198852872751	0.586221737312	-0.00441949670389	0.101774890116	0.00793207245126	-0.0536644668093	-0.00150170155477	-0.00386674539954	-0.0642947765165	0.0147302181569	0.000162380460308	0.137905682777	-0.00422311344543	0.00182852924123	0.124512969901	0.0115301887508	0.131198194497	-19.9031506521	-8.79176962329	2.86306190197
16	3.42854884021	0.785879425934	-1.68475308209	1.60181342956	-0.971697833968	3.74175786677	-0.0340633127566	0.234694536242	-0.054230347418	-0.102179074335	0.0370455364871	0.136755245584	0.0786691198481	-0.266164440725	-0.0130450155358	0.100435477019	0.0220311656501	-0.0214651294543	0.107786947024	-0.0118585770709	0.144930812633	-43.7103780216	-12.4455648345	2.5722850839
17	0.231540227975	0.011233349134	0.0936391912434	0.810948747102	-0.46747901635	0.795315955027	0.0123640165584	0.0489375572528	0.00615329814389	-0.025411162193	-0.0293048243057	-0.0705391284046	0.0160739200582	0.070725182722	0.0172315223341	0.176041367555	0.00552088915489	0.0144314120311	0.213344806809	-0.00284444161498	0.15566717297	41.1029722131	-15.7043442429	83.2639342523

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 'D' and (resid 120 through 194 )	D	Q	120 - 194	91 - 165
2	2	chain 'D' and (resid 195 through 478 )	D	Q	195 - 478	166 - 449
3	3	chain 'D' and (resid 479 through 526 )	D	Q	479 - 526	450 - 497
4	4	chain 'A' and (resid 31 through 119 )	A	A	31 - 119	1 - 89
5	5	chain 'A' and (resid 120 through 194 )	A	A	120 - 194	90 - 164
6	6	chain 'A' and (resid 195 through 496 )	A	A	195 - 496	165 - 466
7	7	chain 'A' and (resid 497 through 527 )	A	A	497 - 527	467 - 497
8	8	chain 'B' and (resid 30 through 119 )	B	F	30 - 119	1 - 90
9	9	chain 'B' and (resid 120 through 194 )	B	F	120 - 194	91 - 165
10	10	chain 'B' and (resid 195 through 496 )	B	F	195 - 496	166 - 467
11	11	chain 'B' and (resid 497 through 535 )	B	F	497 - 535	468 - 506
12	12	chain 'C' and (resid 30 through 119 )	C	K	30 - 119	1 - 90
13	13	chain 'C' and (resid 120 through 194 )	C	K	120 - 194	91 - 165
14	14	chain 'C' and (resid 195 through 287 )	C	K	195 - 287	166 - 258
15	15	chain 'C' and (resid 288 through 478 )	C	K	288 - 478	259 - 449
16	16	chain 'C' and (resid 479 through 525 )	C	K	479 - 525	450 - 496
17	17	chain 'D' and (resid 30 through 119 )	D	Q	30 - 119	1 - 90

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