PDB-3lj7: 3D-crystal structure of humanized-rat fatty acid amide hydrolase ...

ID or keywords:

Entry

Database: PDB / ID: 3lj7

Title

3D-crystal structure of humanized-rat fatty acid amide hydrolase (FAAH) conjugated with Carbamate inhibitor URB597

Components

Fatty-acid amide hydrolase 1

Keywords

HYDROLASE / protein-inhibitor complex / FAAH / fatty acid amide hydrolase / carbamate / inhibitor / covalent / Endoplasmic reticulum / Golgi apparatus / Membrane / Transmembrane

Function / homology

Function and homology information

Arachidonate metabolism / fatty acid amide hydrolase / regulation of trans-synaptic signaling by endocannabinoid, modulating synaptic transmission / fatty acid amide hydrolase activity / monoacylglycerol catabolic process / monoacylglycerol lipase activity / amidase activity / fatty acid catabolic process / Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / hydrolase activity, acting on ester bonds ...
Similarity search - Function

Biological species

Rattus norvegicus (Norway rat)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.3 Å

Authors

Mileni, M. / Stevens, R.C. / Kamtekar, S.

Citation

Journal: J.Mol.Biol. / Year: 2010
Title: Crystal structure of fatty acid amide hydrolase bound to the carbamate inhibitor URB597: discovery of a deacylating water molecule and insight into enzyme inactivation
Authors: Mileni, M. / Kamtekar, S. / Wood, D.C. / Benson, T.E. / Cravatt, B.F. / Stevens, R.C.

History

Deposition	Jan 25, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 9, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Oct 13, 2021	Group: Database references / Derived calculations Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3	Sep 6, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4	Nov 20, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3lj7.cif.gz	439.1 KB	Display	PDBx/mmCIF format
PDB format	pdb3lj7.ent.gz	359.4 KB	Display	PDB format
PDBx/mmJSON format	3lj7.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/lj/3lj7 ftp://data.pdbj.org/pub/pdb/validation_reports/lj/3lj7	HTTPS FTP

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Related structure data

Related structure data	3lj6C 2wj1S 2vya 2wap C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6mrg-4 6mrg-3 6mrg-2 4zgx-5 4zgx-4 4dl1-10 3mzs-3 3lj6-2 4yed-2 5ulj-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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: Fatty-acid amide hydrolase 1

B: Fatty-acid amide hydrolase 1

hetero molecules

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

1

A: Fatty-acid amide hydrolase 1

hetero molecules

defined by author
63.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Fatty-acid amide hydrolase 1

hetero molecules

defined by author
63.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	102.733, 105.075, 147.802
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Fatty-acid amide hydrolase 1 / Oleamide hydrolase 1 / Anandamide amidohydrolase 1 Mass: 63111.664 Da / Num. of mol.: 2 / Fragment: deltaTM-FAAH (UNP residues 30-579) Mutation: Trans-membrane deletion (1-30); L192F, F194Y, A377T, S435N, I491V, V495M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Faah, Faah1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 References: UniProt: P97612, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#2: Chemical	ChemComp-OHO / CYCLOHEXANE AMINOCARBOXYLIC ACID Mass: 143.184 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₇H₁₃NO₂
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 481 / Source method: isolated from a natural source / Formula: H₂O
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: 3.16 Å³/Da / Density % sol: 61.08 %
Crystal grow	Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 30% PEG400, 100 mM TrisHCl, 100 mM MgCl2, 100 mM NaCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 287K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03317 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 12, 2008
Radiation	Monochromator: double crystal monochromator and K-B pair of biomorph mirrors for vertical and horizontal focusing Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.03317 Å / Relative weight: 1
Reflection	Resolution: 2.3→30 Å / Num. all: 70007 / Num. obs: 70007 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / B_iso Wilson estimate: 46.8 Å² / R_merge(I) obs: 0.07 / Net I/σ(I): 10.6
Reflection shell	Resolution: 2.3→2.4 Å / Redundancy: 3.3 % / R_merge(I) obs: 0.52 / Mean I/σ(I) obs: 2.2 / % possible all: 98.5

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Processing

Software

Name	Version	Classification
XDS	package	data scaling
PHASER		phasing
PHENIX	(phenix.refine)	refinement
XDS	package	data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WJ1

2wj1

Resolution: 2.3→29.795 Å / SU ML: 0.32 / Isotropic thermal model: isotropic / σ(F): 2 / Phase error: 20.71 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2142	3549	5.07 %
R_work	0.1763	-	-
obs	0.1782	70004	97.69 %
all	-	70007	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 39.978 Å² / k_sol: 0.318 e/Å³

Displacement parameters

B_iso mean: 45.2 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→29.795 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8428	0	20	481	8929

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.012	8663
X-RAY DIFFRACTION	f_angle_d	1.282	11754
X-RAY DIFFRACTION	f_dihedral_angle_d	19.81	3242
X-RAY DIFFRACTION	f_chiral_restr	0.075	1317
X-RAY DIFFRACTION	f_plane_restr	0.007	1525

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 (%)
2.3-2.3315	0.2992	163	0.27	2626	X-RAY DIFFRACTION	98
2.3315-2.3648	0.2897	136	0.2491	2646	X-RAY DIFFRACTION	99
2.3648-2.4001	0.288	128	0.242	2667	X-RAY DIFFRACTION	98
2.4001-2.4376	0.2675	154	0.2254	2631	X-RAY DIFFRACTION	99
2.4376-2.4775	0.2527	150	0.2119	2643	X-RAY DIFFRACTION	99
2.4775-2.5202	0.2643	135	0.215	2655	X-RAY DIFFRACTION	98
2.5202-2.566	0.2898	130	0.2091	2692	X-RAY DIFFRACTION	99
2.566-2.6153	0.2345	130	0.1981	2659	X-RAY DIFFRACTION	99
2.6153-2.6687	0.2794	143	0.202	2672	X-RAY DIFFRACTION	99
2.6687-2.7267	0.2551	144	0.1892	2634	X-RAY DIFFRACTION	98
2.7267-2.7901	0.2403	141	0.1878	2682	X-RAY DIFFRACTION	98
2.7901-2.8598	0.244	126	0.1828	2660	X-RAY DIFFRACTION	98
2.8598-2.937	0.2556	127	0.1869	2682	X-RAY DIFFRACTION	98
2.937-3.0234	0.2434	166	0.1907	2623	X-RAY DIFFRACTION	98
3.0234-3.1209	0.2477	145	0.1806	2658	X-RAY DIFFRACTION	98
3.1209-3.2323	0.2325	137	0.1823	2644	X-RAY DIFFRACTION	98
3.2323-3.3615	0.2113	152	0.1743	2661	X-RAY DIFFRACTION	98
3.3615-3.5143	0.2088	136	0.1711	2660	X-RAY DIFFRACTION	97
3.5143-3.6992	0.169	146	0.1595	2642	X-RAY DIFFRACTION	97
3.6992-3.9305	0.1985	160	0.1578	2645	X-RAY DIFFRACTION	97
3.9305-4.2332	0.1806	147	0.1622	2650	X-RAY DIFFRACTION	97
4.2332-4.6578	0.1878	145	0.1481	2641	X-RAY DIFFRACTION	96
4.6578-5.3284	0.1538	136	0.136	2676	X-RAY DIFFRACTION	96
5.3284-6.7007	0.1861	149	0.1544	2671	X-RAY DIFFRACTION	95
6.7007-29.7978	0.155	123	0.1348	2735	X-RAY DIFFRACTION	93

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	-0.67	-0.1592	-2.4401	1.5319	0.8065	1.7603	-0.1058	0.3421	-0.3537	-0.4031	0.0678	-0.136	0.1175	-0.202	0.162	0.4063	-0.0388	0.1116	0.4844	-0.116	0.2616	18.6827	24.507	-17.3909
2	1.7659	0.0993	0.758	0.8759	1.1532	-0.0784	-0.0504	0.7299	-0.2121	-0.2553	0.0722	0.1004	-0.0193	-0.2556	-0.0071	0.3896	-0.1243	0.0235	0.5916	-0.0827	0.2838	2.0515	26.8146	-16.5269
3	0.4496	-0.2424	-1.3202	0.631	0.4095	0.6693	-0.2157	-0.23	-0.1183	-0.0217	0.1188	-0.1687	0.1617	0.0441	0.1126	0.2779	-0.0274	0.0481	0.2729	-0.0333	0.2798	14.2765	24.9816	-2.4604
4	0.793	0.1456	-0.1958	0.5663	0.4306	0.3749	-0.0272	0.2265	0.0239	-0.1568	0.0556	-0.0515	-0.0168	-0.0185	-0.0305	0.2961	-0.0442	0.0527	0.3419	-0.0266	0.249	10.5389	35.9601	-2.626
5	0.3162	0.1565	-0.0031	0.9888	0.4567	-0.9089	0.0189	0.0046	0.0265	-0.0182	-0.0758	0.0612	-0.0323	-0.141	0.0667	0.3132	-0.0286	0.0171	0.4133	-0.0307	0.2619	-3.5456	31.761	2.5056
6	1.7455	-0.3885	0.1914	0.86	0.2792	1.6682	-0.0809	0.0922	0.1474	-0.1248	0.0995	-0.0929	-0.3662	0.0022	-0.014	0.2976	-0.0377	0.0311	0.1394	0.0268	0.2012	8.1455	50.5383	5.0632
7	2.0758	-0.1574	0.066	0.3895	-0.398	0.8466	-0.0026	-0.3227	0.3383	0.3518	0.095	-0.0423	-0.3177	0.0536	-0.0364	0.2854	-0.1086	0.0128	0.2012	-0.1118	0.275	22.394	50.3304	19.9027
8	1.1524	-0.0164	-0.1758	0.744	0.5951	0.941	0.0288	0.159	0.2379	-0.1823	0.0352	0.0114	-0.3527	-0.0785	-0.0584	0.3318	-0.0195	0.0425	0.2095	0.0557	0.1969	5.1229	52.6291	0.6161
9	5.8144	0.1943	0.5908	0.2115	0.1531	1.0557	-0.3814	-0.8108	0.1318	0.522	0.1663	0.0594	-0.4886	-0.2387	0.207	0.7066	0.11	0.0911	0.451	-0.0722	0.3865	-15.5694	43.6418	53.2384
10	1.917	-1.138	-0.9606	1.8582	-0.4984	1.6113	-0.0645	0.0724	0.2591	0.1287	0.0118	0.1939	-0.3347	-0.4048	0.0378	0.3245	0.0657	0.0956	0.353	0.0332	0.2727	-25.2919	36.8529	40.7014
11	2.0364	0.7788	0.6151	-0.9732	-0.1029	0.7613	0.005	-0.1739	0.2868	0.2736	0.0114	0.0464	-0.7149	0.0129	-0.0069	0.5305	0.0493	0.0544	0.2524	-0.0206	0.3767	-8.0618	44.1815	40.0683
12	0.7704	-0.2461	0.0607	0.4077	0.4255	0.5973	0.0449	-0.1059	0.0611	0.1828	0.0412	-0.0659	-0.1447	-0.0513	-0.0903	0.3515	0.0038	0.0355	0.2336	0.0054	0.2374	-7.1785	32.7364	38.5881
13	-0.3418	-0.144	-0.9659	0.8347	-0.6289	1.7689	0.0602	0.0387	0.0642	0.0289	0.0439	0.1084	-0.1202	-0.1941	-0.1099	0.2647	0.011	0.0471	0.3585	0.0185	0.2594	-13.5051	33.5025	24.3342
14	0.7224	0.1354	-0.196	0.7966	-0.2478	1.3914	-0.0093	-0.0679	-0.1363	-0.0464	-0.0581	-0.0977	0.1292	-0.013	0.0559	0.2537	-0.0204	0.017	0.1612	-0	0.2415	1.2931	19.4634	33.249
15	-1.9086	-0.2802	-0.4893	0.4552	-0.2552	0.7318	-0.0705	0.1787	0.0285	-0.0725	-0.027	-0.4489	-0.0018	0.3489	0.096	0.1593	0.004	-0.017	0.281	0.0645	0.3776	20.8317	25.9517	33.5258
16	0.7912	-0.0703	-0.4211	0.979	-0.3882	0.7723	-0.0928	0.023	-0.094	0.0714	0.036	-0.0507	0.0671	-0.0799	0.0566	0.2485	-0.0349	0.0125	0.1703	0.0013	0.1898	-3.1688	15.9659	34.2956

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 32:70)
2	X-RAY DIFFRACTION	2	(chain A and resid 71:134)
3	X-RAY DIFFRACTION	3	(chain A and resid 135:165)
4	X-RAY DIFFRACTION	4	(chain A and resid 166:276)
5	X-RAY DIFFRACTION	5	(chain A and resid 277:315)
6	X-RAY DIFFRACTION	6	(chain A and resid 316:410)
7	X-RAY DIFFRACTION	7	(chain A and resid 411:451)
8	X-RAY DIFFRACTION	8	(chain A and resid 452:577)
9	X-RAY DIFFRACTION	9	(chain B and resid 32:70)
10	X-RAY DIFFRACTION	10	(chain B and resid 71:134)
11	X-RAY DIFFRACTION	11	(chain B and resid 135:165)
12	X-RAY DIFFRACTION	12	(chain B and resid 166:276)
13	X-RAY DIFFRACTION	13	(chain B and resid 277:315)
14	X-RAY DIFFRACTION	14	(chain B and resid 316:410)
15	X-RAY DIFFRACTION	15	(chain B and resid 411:451)
16	X-RAY DIFFRACTION	16	(chain B and resid 452:577)

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