PDB-9y3k: Crystal Structure of Human Ornithine Aminotransferase Pre-Inactiv...

ID or keywords:

Entry

Database: PDB / ID: 9y3k

Title

Crystal Structure of Human Ornithine Aminotransferase Pre-Inactivated by CPP115 (Tight Binding)

Components

Ornithine aminotransferase, mitochondrial

Keywords

TRANSFERASE / Mechanism based inactivator / aminotransferase

Function / homology

Function and homology information

: / ornithine aminotransferase / L-ornithine transaminase activity / : / Glutamate and glutamine metabolism / L-proline biosynthetic process / visual perception / pyridoxal phosphate binding / mitochondrial matrix / mitochondrion ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.15 Å

Authors

Corrigan, M.C. / Vargas, A.L. / Kang, K.M. / Silverman, R.B. / Liu, D.

Funding support

United States, 4items

Organization	Grant number	Country
National Institutes of Health/National Cancer Institute (NIH/NCI)	R01 DA030604	United States
National Institutes of Health/National Cancer Institute (NIH/NCI)	R01 CA260250	United States
National Institutes of Health/National Cancer Institute (NIH/NCI)	P41 GM108569	United States
National Institutes of Health/National Cancer Institute (NIH/NCI)	P30 DA018310	United States

Citation

Journal: J.Am.Chem.Soc. / Year: 2026
Title: Targeting Conformational Flexibility of a Reactive Intermediate to Enhance Selectivity of a GABA Aminotransferase Inactivator.
Authors: Kang, K.M. / Vargas, A.L. / Ferreira, L.A. / Des Soye, B.J. / Corrigan, M. / Zhang, C.K. / Wang, F. / Duan, D. / Kelleher, N.L. / Hohmann, A.G. / Liu, D. / Silverman, R.B.

History

Deposition	Sep 2, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 22, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9y3k.cif.gz	593.3 KB	Display	PDBx/mmCIF format
PDB format	pdb9y3k.ent.gz	407.4 KB	Display	PDB format
PDBx/mmJSON format	9y3k.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/y3/9y3k ftp://data.pdbj.org/pub/pdb/validation_reports/y3/9y3k	HTTPS FTP

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Related structure data

Related structure data	9y3mC 9y53C C: citing same article (ref.)
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

Deposited unit

A: Ornithine aminotransferase, mitochondrial

B: Ornithine aminotransferase, mitochondrial

C: Ornithine aminotransferase, mitochondrial

hetero molecules

136 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Ornithine aminotransferase, mitochondrial

hetero molecules

A: Ornithine aminotransferase, mitochondrial

hetero molecules

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

2

B: Ornithine aminotransferase, mitochondrial

C: Ornithine aminotransferase, mitochondrial

hetero molecules

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

Unit cell

Length a, b, c (Å)	115.710, 115.710, 187.500
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	154
Space group name H-M	P3₂21
Space group name Hall	P3₂2"
Symmetry operation	#1: x,y,z #2: -y,x-y,z+2/3 #3: -x+y,-x,z+1/3 #4: x-y,-y,-z+1/3 #5: -x,-x+y,-z+2/3 #6: y,x,-z

Components on special symmetry positions

ID	Model	Components
1	1	A-668- HOH
2	1	A-760- HOH
3	1	B-752- HOH
4	1	B-796- HOH

#1: Protein	Ornithine aminotransferase, mitochondrial / Ornithine delta-aminotransferase / Ornithine--oxo-acid aminotransferase Mass: 44860.320 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: OAT / Plasmid: BL21DE3 / Production host: Escherichia coli (E. coli) / References: UniProt: P04181, ornithine aminotransferase
#2: Chemical	ChemComp-RW2 / (1S)-4-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]cyclopent-3-ene-1,3-dicarboxylic acid Mass: 402.293 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₅H₁₉N₂O₉P
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 527 / Source method: isolated from a natural source / Formula: H₂O
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: 2.69 Å³/Da / Density % sol: 54.32 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 10% PEG 6000, 100 mM Nacl, 14% glycerol, pH 7.8

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.978 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 6, 2025
Radiation	Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.978 Å / Relative weight: 1
Reflection	Resolution: 2.15→55.28 Å / Num. obs: 79584 / % possible obs: 100 % / Redundancy: 11.2 % / B_iso Wilson estimate: 40.02 Å² / CC_1/2: 0.999 / Net I/σ(I): 15.8
Reflection shell	Resolution: 2.15→2.21 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 5828 / CC_1/2: 0.498

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.15→53.03 Å / SU ML: 0.2163 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.8976
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2038	4159	5.23 %
R_work	0.1608	75358	-
obs	0.1631	79517	99.98 %

Solvent computation

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

Displacement parameters

B_iso mean: 51.91 Å²

Refinement step

Cycle: LAST / Resolution: 2.15→53.03 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9467	0	81	527	10075

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0079	9773
X-RAY DIFFRACTION	f_angle_d	0.9807	13285
X-RAY DIFFRACTION	f_chiral_restr	0.0583	1467
X-RAY DIFFRACTION	f_plane_restr	0.0075	1706
X-RAY DIFFRACTION	f_dihedral_angle_d	16.9236	3669

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 (%)
2.15-2.17	0.2806	120	0.2489	2502	X-RAY DIFFRACTION	100
2.17-2.2	0.3089	147	0.2451	2508	X-RAY DIFFRACTION	100
2.2-2.23	0.3141	128	0.2395	2472	X-RAY DIFFRACTION	100
2.23-2.26	0.2684	119	0.2318	2496	X-RAY DIFFRACTION	100
2.26-2.28	0.2801	158	0.2277	2447	X-RAY DIFFRACTION	99.96
2.28-2.32	0.2644	103	0.2176	2535	X-RAY DIFFRACTION	100
2.32-2.35	0.2749	165	0.2183	2456	X-RAY DIFFRACTION	100
2.35-2.38	0.2283	110	0.2109	2493	X-RAY DIFFRACTION	100
2.38-2.42	0.2386	144	0.2128	2500	X-RAY DIFFRACTION	100
2.42-2.46	0.2705	133	0.2055	2486	X-RAY DIFFRACTION	100
2.46-2.5	0.2768	146	0.1906	2497	X-RAY DIFFRACTION	99.96
2.5-2.55	0.2356	101	0.1774	2487	X-RAY DIFFRACTION	100
2.55-2.6	0.2425	146	0.1897	2502	X-RAY DIFFRACTION	100
2.6-2.65	0.2561	142	0.1854	2474	X-RAY DIFFRACTION	100
2.65-2.71	0.1951	135	0.1799	2520	X-RAY DIFFRACTION	100
2.71-2.77	0.2445	155	0.1711	2488	X-RAY DIFFRACTION	100
2.77-2.84	0.2232	123	0.1788	2497	X-RAY DIFFRACTION	100
2.84-2.92	0.2202	166	0.1667	2470	X-RAY DIFFRACTION	99.96
2.92-3	0.2158	131	0.1734	2494	X-RAY DIFFRACTION	100
3-3.1	0.2178	174	0.1737	2482	X-RAY DIFFRACTION	100
3.1-3.21	0.2344	141	0.1702	2514	X-RAY DIFFRACTION	100
3.21-3.34	0.1879	150	0.1574	2513	X-RAY DIFFRACTION	100
3.34-3.49	0.197	122	0.156	2539	X-RAY DIFFRACTION	100
3.49-3.68	0.1793	129	0.144	2519	X-RAY DIFFRACTION	99.96
3.68-3.91	0.1805	149	0.1406	2524	X-RAY DIFFRACTION	100
3.91-4.21	0.1872	126	0.1249	2531	X-RAY DIFFRACTION	100
4.21-4.63	0.1866	141	0.1205	2567	X-RAY DIFFRACTION	100
4.63-5.3	0.16	168	0.131	2529	X-RAY DIFFRACTION	99.96
5.3-6.68	0.1981	134	0.1638	2617	X-RAY DIFFRACTION	100
6.68-53.03	0.1587	153	0.1463	2699	X-RAY DIFFRACTION	99.55

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	1.4675021643	-0.104034920489	-0.0562385346339	0.229322438896	0.288987902769	0.907874924587	0.12144233738	-0.492218328196	0.278509402834	0.0883368564637	0.0836475882784	-0.421193721546	-0.282806816173	0.478282176773	-0.203162326208	0.329767866339	-0.0455740117062	-0.0272508913091	0.700953699762	-0.178157657855	0.787942482744	9.43312622174	-11.197211462	15.2698523614
2	0.750864989789	-0.360399301865	0.60592219981	0.664883297319	-0.145653018111	1.50066095184	0.201035163672	-0.264739900707	0.115090632622	-0.0106871470465	0.236605960099	-0.350085916264	-0.139808814522	0.375455839754	-0.354436894056	0.371348637228	-0.104958182124	0.09765110052	0.670525132826	-0.146087530148	0.936990713148	15.1683133197	-9.35647945327	2.90936972562
3	0.486104995716	0.518024017278	0.090292438594	0.589394385964	0.350963778268	1.3867970269	0.103103197838	0.0837177823082	0.391870949751	-0.279033998902	-0.0210624354694	-0.0330301663705	-0.426265858286	0.119389593641	-0.0706005991969	0.415134807848	0.0691227237531	0.141970908701	0.35578639998	0.0406545530524	0.635263689562	-6.98607749922	-7.77933408907	-11.9919192203
4	0.635860633532	-0.261677955825	-0.687149664976	0.789392697395	-0.0214737590372	1.25408468815	0.000176988669621	0.0058972101687	0.122354571868	0.0367356223048	-0.0243535161521	-0.173719823567	0.0765854508265	0.124050037385	0.0218526915754	0.226128359305	0.0968548217993	0.0392946921504	0.348054910232	-0.00622684884973	0.362160033781	-8.66126629573	-31.2883451961	-4.49287748551
5	1.43974081036	0.790576130927	-0.15283192625	1.23975782335	-0.260632589615	0.738745405529	0.0203873875526	0.0983504311667	0.139713623312	-0.207126412643	-0.0274420575825	-0.301758535443	-0.0176332823329	0.160397915571	0.00970962714927	0.285279054452	0.103496497455	0.102457486028	0.430935635718	0.0117387729945	0.446315051571	0.631514118456	-29.4145214622	-15.2343664544
6	1.44716419477	0.577330344514	-0.064428331438	0.726401371602	0.367996432406	1.74707807922	0.141655625966	0.102673648502	0.274995367742	-0.166200218819	0.0026542793632	-0.216482562167	-0.222542816143	0.313545853058	-0.128586370855	0.321143174859	0.0290003184076	0.129224530329	0.354378118511	0.0262236482214	0.552072304312	5.13248529154	-15.4649421461	-11.6972775171
7	0.961071085975	0.108133539769	0.307275028912	0.919811593682	1.44660935081	3.50547806009	0.0961833554287	-0.292102118591	0.2766131831	0.397816411297	0.00710468754431	-0.418260818879	0.682883131832	0.361441094129	-0.102706349525	0.335811239345	0.0498572457789	-0.0522625236269	0.695176674305	-0.0665312591299	0.737364907446	18.3209718744	-26.2878015118	6.08065696606
8	1.37268551725	-0.530331969973	0.92583862469	0.826196335173	0.267238888249	1.24143986379	-0.0730936242535	-0.333748402209	0.0787627201593	0.020254836757	0.315773601379	-0.296183155247	-0.207998118247	0.609413855171	-0.198999666315	0.284522002949	-0.0629910708607	0.0863362142434	0.890768100565	-0.124733880354	0.945898934235	24.8787057652	-17.968362088	-0.310199939753
9	1.0079846679	-0.37128742195	0.756465026509	0.596857857032	-0.0914684274152	1.86414990829	0.0436321019945	0.337675929875	-0.0261464793656	-0.128167465877	-0.0387892986353	-0.405462357443	0.272257230721	0.685685010596	-0.0475178465536	0.503386170211	0.236807659268	0.0702751459223	0.622026059667	-0.0453013266194	0.51860686196	17.299035706	-70.0400109328	-16.6519484659
10	1.69440535929	-0.654750229823	-0.133704987728	1.20318594346	0.365445152799	0.595481093447	0.118525652646	0.0309132732127	-0.125086894881	0.175489690951	0.00333965549198	-0.16013442737	0.445303055957	0.20797783985	-0.0878253795433	0.547027049993	0.224478589843	0.00463818587686	0.458805095394	0.0167151054712	0.316768865789	3.66901261984	-77.8755879099	-0.628082289065
11	0.126901138864	-0.12457965881	0.196996332071	1.09847247918	0.191000241756	1.3980909785	-0.0179547223628	-0.0155549657947	0.0810981389757	-0.0505053892278	-0.0282970370974	-0.0369384663296	0.125508399955	-0.0138745861945	0.0427603170734	0.283342468715	0.12666548769	0.0252165633013	0.391132335793	-0.0312884951463	0.284630908139	-9.64183193397	-55.1346507077	-4.16273759606
12	0.767207288039	-0.164900143513	0.110946919839	2.2789773931	0.117653992416	1.09942733007	-0.00841468741678	-0.104107698544	0.0206644253713	0.219553662454	-0.0371787139352	-0.0197490281805	0.153595325322	0.0490042216129	0.0338922326065	0.331468735497	0.130252603317	0.00544461683019	0.412678153647	-0.0220983230245	0.251955621318	-4.87128979413	-56.9180792971	6.64018104092
13	2.45481671475	0.895157980112	0.119277263515	1.39513515077	0.433133375897	1.49190015716	0.0694012179716	-0.232386376363	0.163240690742	0.120684422918	-0.0946513772154	-0.0812689385995	0.293692071603	0.163807760119	-0.0219776616025	0.407312480794	0.207959058869	3.90264416923E-5	0.378093738278	-0.0108513335561	0.343077409031	6.87325252468	-66.5729200601	5.54030430506
14	1.15008611786	-0.0249830240081	-0.549226309892	0.699556871115	1.25091841646	2.25776483366	0.193777442118	0.256542304514	0.544365423813	-0.374460117931	0.137857692536	-0.35433829843	-0.339035809646	0.405968257514	-0.271809051365	0.442753159165	0.162878914457	0.115804787653	0.686965675722	0.0372986248544	0.626670154186	21.0132448275	-54.6896013113	-4.84308958879
15	1.86396814867	0.685753310232	-0.382629522737	1.54271535855	0.441304129652	1.35889727444	0.128757972501	0.0568868878429	-0.149901040029	0.164084767646	0.138272652225	-0.540242031536	0.100148513696	0.670423781749	-0.320524090664	0.353578047403	0.193369288855	-0.046391982665	0.710938181356	-0.0652075913553	0.555617751835	24.4909642904	-62.6466676819	3.84454455874
16	0.701459798549	-0.15630015494	0.195483257211	1.60931767645	0.201680587901	1.29981384175	-0.0648896186794	-0.396989698409	-0.341271595715	0.380899851751	0.0384380994887	0.248775054484	0.618092743611	-0.0774774659017	0.0518793608114	0.722623864766	-0.043972973793	0.0400263728505	0.602747770368	0.0800593498149	0.585575715336	-17.0134688582	-84.6400205442	0.584177902824
17	0.543194099335	0.173028244496	0.282941817555	1.663766179	-0.395150448236	1.03268939171	-0.0315479337039	0.0125420836622	-0.136043483765	-0.154398715306	0.0341966860274	-0.159365381313	0.666414185741	0.176496074182	0.0060608834758	0.704706770331	0.174574527458	0.030660278529	0.374132643087	-0.0388479199688	0.37345271939	0.180722671024	-83.2405478673	-13.8434009118
18	0.206309153214	0.050393544153	-0.0565796986601	1.17198497435	0.392399752323	1.88453554809	0.0168890070955	0.0336340090685	0.10876524926	-0.0751055799847	0.00881965498776	0.139864850638	0.222613220521	-0.321453296994	-0.0264993970394	0.391327369592	0.0853783163144	0.0212256781526	0.449882363707	0.00787664846337	0.291124506769	-13.4436550111	-61.8512740325	-24.3400630543
19	0.866991618202	-0.0282394326399	0.0314112041895	1.34884279233	-0.389837814766	1.57711127746	-0.0261662718263	0.187460843361	-0.0894789604042	-0.324570240206	0.0695221967049	-0.0821533952449	0.37821863224	-0.103714695304	-0.0283981482877	0.509305049143	0.0939920683765	0.0294525808086	0.376620560434	-0.0426163842302	0.259601172408	-6.84986504118	-71.2910105064	-29.3558031944
20	1.42997088645	0.483146956695	0.0620477327432	2.19075761417	-0.172131675825	1.59797695582	-0.0710023199854	0.231687016041	-0.279526189612	-0.210091548574	0.221889220764	0.0273468727501	0.797907478374	-0.0588327598479	-0.122032825194	0.678602541878	0.0443439277954	0.000240288116827	0.379924519312	-0.0287775365868	0.272901483343	-10.8421328287	-83.1100606788	-23.4881024351
21	0.245011249277	0.0251828366517	-0.378221197142	0.101218191641	0.208921903139	1.19252841941	-0.21778927333	-0.0213656003186	0.794017661074	0.168474381683	-0.0568811817295	0.446483016929	0.505268356359	-0.732117114138	0.206277495948	0.774502757095	-0.139690910991	0.0431036370492	0.916027896543	0.181679172195	0.972472348804	-33.5664426751	-86.2662797733	-12.3223874915
22	1.90902130166	0.147205245635	-0.0481586071761	1.49731098422	-0.010197360795	2.22700531329	0.119043048484	-0.252071064062	-0.220034380699	-0.246570285623	0.140206329837	0.368699404646	0.871514804929	-0.740487231211	-0.276766495369	0.940286382557	-0.171869528019	-0.0562613419478	0.550844100128	0.043970409033	0.590963192893	-23.4096020169	-91.9928409574	-18.0884385294

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 37 through 70 )	A	A	37 - 70	1 - 34
2	2	chain 'A' and (resid 71 through 95 )	A	A	71 - 95	35 - 59
3	3	chain 'A' and (resid 96 through 158 )	A	A	96 - 158	60 - 122
4	4	chain 'A' and (resid 159 through 212 )	A	A	159 - 212	123 - 176
5	5	chain 'A' and (resid 213 through 276 )	A	A	213 - 276	177 - 240
6	6	chain 'A' and (resid 277 through 371 )	A	A	277 - 371	241 - 335
7	7	chain 'A' and (resid 372 through 411 )	A	A	372 - 411	336 - 375
8	8	chain 'A' and (resid 412 through 439 )	A	A	412 - 439	376 - 403
9	9	chain 'B' and (resid 37 through 70 )	B	C	37 - 70	1 - 34
10	10	chain 'B' and (resid 71 through 130 )	B	C	71 - 130	35 - 94
11	11	chain 'B' and (resid 131 through 212 )	B	C	131 - 212	95 - 176
12	12	chain 'B' and (resid 213 through 313 )	B	C	213 - 313	177 - 277
13	13	chain 'B' and (resid 314 through 371 )	B	C	314 - 371	278 - 335
14	14	chain 'B' and (resid 372 through 411 )	B	C	372 - 411	336 - 375
15	15	chain 'B' and (resid 412 through 439 )	B	C	412 - 439	376 - 403
16	16	chain 'C' and (resid 37 through 70 )	C	E	37 - 70	1 - 34
17	17	chain 'C' and (resid 71 through 130 )	C	E	71 - 130	35 - 94
18	18	chain 'C' and (resid 131 through 245 )	C	E	131 - 245	95 - 209
19	19	chain 'C' and (resid 246 through 313 )	C	E	246 - 313	210 - 277
20	20	chain 'C' and (resid 314 through 380 )	C	E	314 - 380	278 - 344
21	21	chain 'C' and (resid 381 through 399 )	C	E	381 - 399	345 - 363
22	22	chain 'C' and (resid 400 through 439 )	C	E	400 - 439	364 - 403

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