PDB-5qcr: Crystal structure of BACE complex with BMC026

ID or keywords:

Entry

Database: PDB / ID: 5qcr

Title

Crystal structure of BACE complex with BMC026

Components

Beta-secretase 1

Keywords

HYDROLASE / Hydroloase / D3R / BACE / Ligand Docking

Function / homology

Function and homology information

memapsin 2 / Golgi-associated vesicle lumen / signaling receptor ligand precursor processing / beta-aspartyl-peptidase activity / amyloid precursor protein catabolic process / amyloid-beta formation / membrane protein ectodomain proteolysis / amyloid-beta metabolic process / cellular response to manganese ion / prepulse inhibition ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.2 Å

Model details

Structures for D3R docking challenge

Authors

Rondeau, J.M. / Shao, C. / Yang, H. / Burley, S.K.

Citation

Journal: J.Comput.Aided Mol.Des. / Year: 2020
Title: D3R grand challenge 4: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies.
Authors: Parks, C.D. / Gaieb, Z. / Chiu, M. / Yang, H. / Shao, C. / Walters, W.P. / Jansen, J.M. / McGaughey, G. / Lewis, R.A. / Bembenek, S.D. / Ameriks, M.K. / Mirzadegan, T. / Burley, S.K. / Amaro, R.E. / Gilson, M.K.

History

Deposition	Dec 1, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 3, 2020	Provider: repository / Type: Initial release
Revision 1.1	Dec 30, 2020	Group: Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.2	Feb 10, 2021	Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID
Revision 1.3	Nov 13, 2024	Group: Data collection / Database references / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5qcr.cif.gz	460.2 KB	Display	PDBx/mmCIF format
PDB format	pdb5qcr.ent.gz	380.6 KB	Display	PDB format
PDBx/mmJSON format	5qcr.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5qcr_validation.pdf.gz	1.2 MB	Display	wwPDB validaton report
Full document	5qcr_full_validation.pdf.gz	1.2 MB	Display
Data in XML	5qcr_validation.xml.gz	42.7 KB	Display
Data in CIF	5qcr_validation.cif.gz	60.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qc/5qcr ftp://data.pdbj.org/pub/pdb/validation_reports/qc/5qcr	HTTPS FTP

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Group deposition

ID	G_1002044 (26 entries) 5qco 5qcp 5qcq 5qcr 5qcs 5qct 5qcu 5qcv 5qcw 5qcx
Title	Crystal Structures of Beta-Secretase 1 with Bound Ligands
Type	undefined
Description	Crystal Structures of Complexes of Beta-Secretase 1 and Ligands

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Related structure data

Similar structure data	4lxm-1 2vj7-d 3rtn-d 4lxk-3 6nv7-3 3dv1-3 4dus-d 2f3f-3 3k5c-2 5qd7-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#115 - Jul 2009 beta-Secretase similarity (5) #79 - Jul 2006 Amyloid-beta Precursor Protein similarity (5)

Deposited unit

A: Beta-secretase 1

B: Beta-secretase 1

C: Beta-secretase 1

hetero molecules

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

1

A: Beta-secretase 1

hetero molecules

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

2

B: Beta-secretase 1

hetero molecules

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

3

C: Beta-secretase 1

hetero molecules

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

Unit cell

Length a, b, c (Å)	81.761, 102.757, 99.928
Angle α, β, γ (deg.)	90.00, 103.28, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID
1	1
2	1
3	1

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Selection details
1	1	1	CHAIN A
2	1	1	CHAIN B
3	1	1	CHAIN C

#1: Protein	Beta-secretase 1 / Aspartyl protease 2 / Asp 2 / Beta-site amyloid precursor protein cleaving enzyme 1 / Beta-site APP ...Aspartyl protease 2 / Asp 2 / Beta-site amyloid precursor protein cleaving enzyme 1 / Beta-site APP cleaving enzyme 1 / Memapsin-2 / Membrane-associated aspartic protease 2 Mass: 44777.336 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BACE1, BACE, KIAA1149 / Production host: Escherichia coli (E. coli) / References: UniProt: P56817, memapsin 2
#2: Chemical	ChemComp-E4J / 2-(butylamino)-N-[(2S,3S,5R)-6-(butylamino)-3-hydroxy-5-methyl-6-oxo-1-phenylhexan-2-yl]-6-methoxypyridine-4-carboxamide Mass: 498.657 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂₈H₄₂N₄O₄
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 315 / 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: 3.04 Å³/Da / Density % sol: 59.56 %
Crystal grow	Temperature: 292 K / Method: hanging drop Details: CRYSTALS WERE GROWN AT 19C BY VAPOUR DIFFUSION IN HANGING DROPS USING 1.0M UNBUFFERED AMMONIUM SULFATE AS PRECIPITANT. PROTEIN STOCK WAS BACE MUT46B BATCH IX 8.1MG/ML IN 10MM TRIS-HCL PH 7. ...Details: CRYSTALS WERE GROWN AT 19C BY VAPOUR DIFFUSION IN HANGING DROPS USING 1.0M UNBUFFERED AMMONIUM SULFATE AS PRECIPITANT. PROTEIN STOCK WAS BACE MUT46B BATCH IX 8.1MG/ML IN 10MM TRIS-HCL PH 7.4, 25MM NACL WITH A 4-FOLD EXCESS OF BMC026 ADDED FROM A 100MM STOCK SOLUTION IN DMSO. CRYO-PROTECTANT WAS 2.0M LI2SO4, 2%(V/V) PEG 400, 0.1M CITRATE PH 5.5, 0.5MM BMC026, 1% DMSO.

Crystal

Density Matthews: 3.04 Å³/Da / Density % sol: 59.56 %

Crystal grow

Temperature: 292 K / Method: hanging drop
Details: CRYSTALS WERE GROWN AT 19C BY VAPOUR DIFFUSION IN HANGING DROPS USING 1.0M UNBUFFERED AMMONIUM SULFATE AS PRECIPITANT. PROTEIN STOCK WAS BACE MUT46B BATCH IX 8.1MG/ML IN 10MM TRIS-HCL PH 7. ...

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Data collection

Diffraction	Mean temperature: 95 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9795
Detector	Type: MAR CCD 165 mm / Detector: CCD / Date: Jul 31, 2003
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 2.2→46.52 Å / Num. obs: 81413 / % possible obs: 99.7 % / R_merge(I) obs: 0.059

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
PHENIX	1.12_2829	refinement
CNX		refinement
CNX		phasing
SCALEPACK		data scaling
DENZO		date reduction
PDB_EXTRACT	3.24	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.2→46.52 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.45 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.205	8170	10.04 %
R_work	0.173	-	-
obs	0.176	81413	99.7 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 51 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→46.52 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8859	0	123	315	9297

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	9219
X-RAY DIFFRACTION	f_angle_d	0.981	12528
X-RAY DIFFRACTION	f_dihedral_angle_d	16.087	5373
X-RAY DIFFRACTION	f_chiral_restr	0.064	1353
X-RAY DIFFRACTION	f_plane_restr	0.007	1608

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type
1	1	A	5405	X-RAY DIFFRACTION	POSITIONAL
1	2	B	5405	X-RAY DIFFRACTION	POSITIONAL
1	3	C	5405	X-RAY DIFFRACTION	POSITIONAL

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 (%)
2.2001-2.2251	0.2641	249	0.2034	2288	X-RAY DIFFRACTION	93
2.2251-2.2513	0.2465	290	0.1927	2408	X-RAY DIFFRACTION	100
2.2513-2.2787	0.2385	290	0.1822	2445	X-RAY DIFFRACTION	100
2.2787-2.3076	0.2277	273	0.1923	2402	X-RAY DIFFRACTION	100
2.3076-2.338	0.2603	286	0.1924	2432	X-RAY DIFFRACTION	100
2.338-2.37	0.2544	263	0.1929	2428	X-RAY DIFFRACTION	100
2.37-2.4038	0.2381	280	0.2014	2446	X-RAY DIFFRACTION	100
2.4038-2.4397	0.2374	265	0.195	2444	X-RAY DIFFRACTION	100
2.4397-2.4778	0.2643	266	0.1958	2486	X-RAY DIFFRACTION	100
2.4778-2.5185	0.241	265	0.1818	2413	X-RAY DIFFRACTION	100
2.5185-2.5619	0.2096	275	0.1809	2456	X-RAY DIFFRACTION	100
2.5619-2.6085	0.2452	263	0.1843	2409	X-RAY DIFFRACTION	100
2.6085-2.6586	0.2331	257	0.189	2466	X-RAY DIFFRACTION	100
2.6586-2.7129	0.244	284	0.1948	2431	X-RAY DIFFRACTION	100
2.7129-2.7719	0.2405	251	0.2021	2470	X-RAY DIFFRACTION	100
2.7719-2.8363	0.2608	275	0.2073	2436	X-RAY DIFFRACTION	100
2.8363-2.9073	0.2326	278	0.1975	2436	X-RAY DIFFRACTION	100
2.9073-2.9859	0.2323	294	0.1991	2422	X-RAY DIFFRACTION	100
2.9859-3.0737	0.2401	240	0.1922	2473	X-RAY DIFFRACTION	100
3.0737-3.1729	0.2389	284	0.1986	2447	X-RAY DIFFRACTION	100
3.1729-3.2863	0.2308	262	0.1968	2442	X-RAY DIFFRACTION	100
3.2863-3.4178	0.2069	275	0.1936	2468	X-RAY DIFFRACTION	100
3.4178-3.5733	0.2047	260	0.1726	2474	X-RAY DIFFRACTION	100
3.5733-3.7616	0.1942	267	0.154	2442	X-RAY DIFFRACTION	100
3.7616-3.9972	0.1596	272	0.1379	2445	X-RAY DIFFRACTION	100
3.9972-4.3056	0.1627	279	0.1358	2456	X-RAY DIFFRACTION	100
4.3056-4.7385	0.1437	306	0.1225	2430	X-RAY DIFFRACTION	100
4.7385-5.4233	0.1691	264	0.1434	2482	X-RAY DIFFRACTION	100
5.4233-6.8293	0.2145	295	0.1845	2457	X-RAY DIFFRACTION	100
6.8293-46.5301	0.2073	262	0.1917	2509	X-RAY DIFFRACTION	99

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	0.1546	-0.2175	-0.2227	0.7529	0.0874	0.4168	-0.1371	-0.3337	0.2448	0.3063	0.037	-0.2205	-0.1054	0.104	-0.0001	0.454	-0.0099	-0.0622	0.3344	-0.0313	0.3488	43.7671	10.302	25.1917
2	0.5836	-0.1575	0.2103	0.6881	0.0057	0.3434	0.041	0.165	0.3765	-0.2976	-0.0482	0.0382	-0.1861	0.0191	-0.0001	0.5021	-0.0382	-0.0039	0.3113	0.074	0.4157	41.08	17.3771	11.3284
3	0.8736	-0.0661	0.4056	2.0071	-0.2843	0.8413	0.0025	0.1187	0.1437	-0.0022	-0.0361	-0.1472	-0.152	0.0709	-0.0001	0.3627	-0.033	0.0058	0.3049	0.0141	0.2392	43.6991	5.0366	17.2717
4	0.4183	-0.245	-0.1352	0.9101	-0.185	0.8453	-0.0288	0.0905	-0.0196	-0.1723	0.1034	0.3737	-0.0184	-0.0327	0.0002	0.3367	0.0077	-0.0467	0.3454	0.0193	0.3671	24.0534	-9.8188	16.9791
5	0.5125	0.3786	0.1131	0.9589	-0.5399	0.6599	0.0259	0.0318	0.1461	0.2312	0.1674	0.2716	0.0144	-0.1314	0.0071	0.2719	0.0279	0.1022	0.2904	0.0341	0.3838	19.8516	-6.6318	29.4121
6	0.8347	0.1736	-0.2297	0.332	-0.0792	0.1448	0.0065	0.0854	0.2762	0.1625	-0.0287	0.381	-0.1838	0.0151	-0.0005	0.4102	0.0571	0.0474	0.306	-0.0077	0.467	22.2424	2.5787	28.6962
7	0.5786	0.0342	0.4584	1.2411	-0.4209	0.5226	-0.0541	-0.2307	-0.1075	0.3427	0.0326	0.1205	-0.3069	0.1572	0.0005	0.4046	0.0438	0.0701	0.2776	0.0047	0.2759	36.699	-8.488	29.1601
8	0.303	-0.2837	-0.0303	0.305	-0.0358	0.0672	0.0493	0.0282	-0.3149	-0.1597	-0.0662	0.3553	0.0571	-0.2961	0.0007	0.4067	0.0141	-0.0287	0.3878	-0.0387	0.3632	30.1565	-20.4402	16.8869
9	0.4264	0.0324	0.1184	0.4914	-0.1783	0.1016	0.1293	-0.4137	-0.1763	0.2934	-0.1661	-0.0846	0.0748	-0.248	0	0.3907	-0.0225	-0.0124	0.5245	0.0518	0.3217	17.5444	11.2228	-2.4292
10	0.7319	-0.4385	0.2261	0.4079	0.1409	0.7688	-0.0331	-0.1564	-0.4959	-0.0609	-0.1452	0.2297	0.141	-0.3928	-0.0001	0.2755	-0.0523	0.0343	0.4999	0.0203	0.4786	3.7069	10.7317	-10.1007
11	1.3752	-0.0199	0.6482	0.788	-0.2402	0.9867	0.0714	-0.1662	-0.0819	0.0345	-0.1885	0.2377	-0.1101	-0.3858	-0.0002	0.3025	0.01	-0.0078	0.43	-0.0182	0.3316	9.5489	15.6425	-11.1048
12	0.9862	0.3383	-0.2439	0.5684	0.4307	0.6467	-0.0151	-0.1747	-0.2598	0.1864	-0.0582	-0.1269	-0.0701	0.0467	-0	0.3211	-0.0001	-0.0447	0.3372	0.0612	0.2615	29.8216	19.1512	-8.084
13	1.1319	0.3946	0.2106	0.7419	-0.5456	0.6716	-0.1844	0.2508	-0.2992	-0.2611	0.1468	0.0724	0.0557	-0.0897	-0	0.3047	0.0037	0.0035	0.3022	-0.062	0.3295	30.2695	9.2422	-28.9071
14	0.4392	-0.0902	-0.1433	0.4785	-0.1089	0.7682	-0.0646	0.1477	-0.364	-0.1479	-0.1244	-0.3916	0.1499	0.2686	-0.1589	0.2947	0.0875	0.0288	0.1783	-0.0115	0.5616	36.4625	-0.4772	-20.9525
15	0.3332	-0.0812	-0.0268	0.2721	0.1224	0.1966	0	0.1354	-0.3505	-0.0029	-0.0964	-0.1261	0.3032	-0.2352	-0.0075	0.4453	-0.0175	-0.0428	0.273	0.0002	0.5947	28.0269	-2.922	-17.027
16	1.4306	0.6393	-0.2873	0.5517	0.3946	1.0794	0.0356	-0.0259	-0.2764	-0.0316	-0.0765	-0.1124	0.0998	0.0468	-0.0083	0.2893	0.0203	-0.0404	0.3066	0.063	0.3841	35.8915	15.8518	-19.0783
17	0.2631	0.0812	-0.3702	0.3363	-0.2907	0.6133	0.1317	0.0953	-0.1904	-0.0716	-0.0611	0.2146	0.1109	-0.4726	-0.0006	0.2857	-0.0371	-0.0107	0.487	0.0473	0.4303	-1.1328	-48.4344	37.3401
18	0.4664	0.0736	-0.1923	0.9926	-0.145	0.9884	0.1029	-0.3333	-0.0976	0.2841	-0.1335	0.1583	0.1505	-0.0592	-0.0004	0.3695	-0.0583	0.0261	0.4032	0.1206	0.3834	2.6314	-56.2524	50.9377
19	0.9978	0.3794	-0.2488	0.9438	-0.2904	1.0565	-0.0075	-0.0171	-0.1906	-0.0125	0.0694	-0.0329	0.1999	-0.1539	0	0.3279	0.0175	-0.018	0.3318	0.0628	0.3589	8.0644	-50.2633	37.7109
20	1.1986	-0.0765	-0.3851	0.4759	-0.2467	0.3146	0.2153	-0.2956	0.0407	0.2133	-0.1514	-0.0919	-0.0771	0.1529	-0.0001	0.3631	-0.0367	-0.0005	0.3835	0.0043	0.351	22.188	-31.5341	42.6923
21	0.912	0.6392	-0.1638	0.7325	-0.6245	1.2342	0.1758	-0.0124	0.2376	0.2884	0.0311	0.1758	-0.1881	-0.0562	0.0305	0.293	0.0355	0.1276	0.2585	-0.0114	0.3462	9.0667	-22.8589	41.4699
22	1.1104	0.537	-0.6546	0.336	-0.4195	1.2339	0.0859	-0.0181	0.083	0.09	-0.083	-0.0891	-0.1305	-0.0517	-0.0001	0.2832	0.0358	-0.0151	0.3071	0.0362	0.3003	17.5385	-34.7675	32.7473

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID -2 THROUGH 32 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 33 THROUGH 74 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 75 THROUGH 192 )
4	X-RAY DIFFRACTION	4	CHAIN 'A' AND (RESID 193 THROUGH 251 )
5	X-RAY DIFFRACTION	5	CHAIN 'A' AND (RESID 252 THROUGH 301 )
6	X-RAY DIFFRACTION	6	CHAIN 'A' AND (RESID 302 THROUGH 340 )
7	X-RAY DIFFRACTION	7	CHAIN 'A' AND (RESID 341 THROUGH 368 )
8	X-RAY DIFFRACTION	8	CHAIN 'A' AND (RESID 369 THROUGH 385 )
9	X-RAY DIFFRACTION	9	CHAIN 'B' AND (RESID -2 THROUGH 32 )
10	X-RAY DIFFRACTION	10	CHAIN 'B' AND (RESID 33 THROUGH 74 )
11	X-RAY DIFFRACTION	11	CHAIN 'B' AND (RESID 75 THROUGH 143 )
12	X-RAY DIFFRACTION	12	CHAIN 'B' AND (RESID 144 THROUGH 192 )
13	X-RAY DIFFRACTION	13	CHAIN 'B' AND (RESID 193 THROUGH 251 )
14	X-RAY DIFFRACTION	14	CHAIN 'B' AND (RESID 252 THROUGH 309 )
15	X-RAY DIFFRACTION	15	CHAIN 'B' AND (RESID 310 THROUGH 340 )
16	X-RAY DIFFRACTION	16	CHAIN 'B' AND (RESID 341 THROUGH 385 )
17	X-RAY DIFFRACTION	17	CHAIN 'C' AND (RESID -2 THROUGH 32 )
18	X-RAY DIFFRACTION	18	CHAIN 'C' AND (RESID 33 THROUGH 85 )
19	X-RAY DIFFRACTION	19	CHAIN 'C' AND (RESID 86 THROUGH 192 )
20	X-RAY DIFFRACTION	20	CHAIN 'C' AND (RESID 193 THROUGH 251 )
21	X-RAY DIFFRACTION	21	CHAIN 'C' AND (RESID 252 THROUGH 327 )
22	X-RAY DIFFRACTION	22	CHAIN 'C' AND (RESID 328 THROUGH 385 )

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