PDB-5qcw: Crystal structure of BACE complex with BMC021

ID or keywords:

Entry

Database: PDB / ID: 5qcw

Title

Crystal structure of BACE complex with BMC021

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 / detection of mechanical stimulus involved in sensory perception of pain / amyloid-beta metabolic process / cellular response to manganese ion ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.1 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5qcw.cif.gz	459 KB	Display	PDBx/mmCIF format
PDB format	pdb5qcw.ent.gz	391.8 KB	Display	PDB format
PDBx/mmJSON format	5qcw.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5qcw_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	5qcw_full_validation.pdf.gz	1.1 MB	Display
Data in XML	5qcw_validation.xml.gz	43.9 KB	Display
Data in CIF	5qcw_validation.cif.gz	61.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qc/5qcw ftp://data.pdbj.org/pub/pdb/validation_reports/qc/5qcw	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	1sgz-4 2f3f-1 5qcv-2 5qcu-2 2q11-2 3qi1-d 6eqm-d 2xfk-d 5qcs-1 3dv1-1 3n4l-1 3vg1-d 3skg-3 4try-3 2f3e-2 6c2i-d 4b1d-d 4gid-3 2q11-1 4gmi-d 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
45.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Beta-secretase 1

hetero molecules

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

3

C: Beta-secretase 1

hetero molecules

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

Unit cell

Length a, b, c (Å)	82.027, 102.945, 99.916
Angle α, β, γ (deg.)	90.00, 103.66, 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 AND (RESID -2 THROUGH 384 OR (RESID 385...
2	1	1	(CHAIN B AND RESID -2 THROUGH 385)
3	1	1	(CHAIN C AND (RESID -2 THROUGH 157 OR RESID 169...

#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-AR9 / (2R,4S)-N-butyl-4-[(2S,5S,7R)-2,7-dimethyl-3,15-dioxo-1,4-diazacyclopentadecan-5-yl]-4-hydroxy-2-methylbutanamide / (2R,4S)-N-Butyl-4-((2S,5S,7R)-2,7-dimethyl-3,15-dioxo-1,4diaza-cyclopentadec-5-yl)-4-hydroxy-2-methyl-butyramide Mass: 439.632 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂₄H₄₅N₃O₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 338 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 3.05 Å³/Da / Density % sol: 59.69 %
Crystal grow	Temperature: 292 K / Method: sitting drop / pH: 5.5 Details: PROTEIN STOCK WAS BACE MUT46B (14-447)7.3MG/ML IN 10MM TRIS-HCL PH 7.4, 25MM NACL. CRYSTALLIZATION SOLUTION WAS 1.0M AMMONIUM SULFATE IN WATER (JBS 6 A2). CRYSTALS WERE GROWN BY VAPOR ...Details: PROTEIN STOCK WAS BACE MUT46B (14-447)7.3MG/ML IN 10MM TRIS-HCL PH 7.4, 25MM NACL. CRYSTALLIZATION SOLUTION WAS 1.0M AMMONIUM SULFATE IN WATER (JBS 6 A2). CRYSTALS WERE GROWN BY VAPOR DIFFUSION IN SITTING DROPS IN 96-WELL CORNING MICROTITER PLATES. CRYO-PROTECTANT WAS 80% WELL SOLUTION, 20% 1,2-PROPANEDIOL.

Crystal

Density Matthews: 3.05 Å³/Da / Density % sol: 59.69 %

Crystal grow

Temperature: 292 K / Method: sitting drop / pH: 5.5
Details: PROTEIN STOCK WAS BACE MUT46B (14-447)7.3MG/ML IN 10MM TRIS-HCL PH 7.4, 25MM NACL. CRYSTALLIZATION SOLUTION WAS 1.0M AMMONIUM SULFATE IN WATER (JBS 6 A2). CRYSTALS WERE GROWN BY VAPOR ...

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Data collection

Diffraction	Mean temperature: 95 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.95371
Detector	Type: MAR CCD 165 mm / Detector: CCD / Date: Mar 27, 2003
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.95371 Å / Relative weight: 1
Reflection	Resolution: 2.104→48.86 Å / Num. obs: 93140 / % possible obs: 99.6 % / R_merge(I) obs: 0.056

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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: 2.1→48.86 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 20.41 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.204	9305	9.99 %
R_work	0.174	-	-
obs	0.177	93140	99.6 %

Solvent computation

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

Displacement parameters

B_iso mean: 51.44 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→48.86 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8934	0	93	338	9365

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	9265
X-RAY DIFFRACTION	f_angle_d	0.965	12591
X-RAY DIFFRACTION	f_dihedral_angle_d	15.798	5420
X-RAY DIFFRACTION	f_chiral_restr	0.062	1373
X-RAY DIFFRACTION	f_plane_restr	0.006	1618

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type
1	1	A	5370	X-RAY DIFFRACTION	POSITIONAL
1	2	B	5370	X-RAY DIFFRACTION	POSITIONAL
1	3	C	5370	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 (%)
2.1041-2.128	0.2337	264	0.1997	2458	X-RAY DIFFRACTION	88
2.128-2.153	0.2478	297	0.1884	2787	X-RAY DIFFRACTION	100
2.153-2.1793	0.2388	323	0.1843	2803	X-RAY DIFFRACTION	100
2.1793-2.2068	0.2082	301	0.1842	2794	X-RAY DIFFRACTION	100
2.2068-2.2359	0.222	283	0.1818	2817	X-RAY DIFFRACTION	100
2.2359-2.2665	0.216	316	0.179	2804	X-RAY DIFFRACTION	100
2.2665-2.2989	0.2309	281	0.1844	2775	X-RAY DIFFRACTION	100
2.2989-2.3332	0.2489	313	0.1804	2806	X-RAY DIFFRACTION	100
2.3332-2.3697	0.2414	309	0.191	2800	X-RAY DIFFRACTION	100
2.3697-2.4085	0.2441	330	0.1912	2794	X-RAY DIFFRACTION	100
2.4085-2.45	0.2304	302	0.1873	2804	X-RAY DIFFRACTION	100
2.45-2.4946	0.2205	331	0.1884	2780	X-RAY DIFFRACTION	100
2.4946-2.5426	0.2243	307	0.1803	2787	X-RAY DIFFRACTION	100
2.5426-2.5945	0.217	342	0.1817	2758	X-RAY DIFFRACTION	100
2.5945-2.6509	0.2171	330	0.1958	2817	X-RAY DIFFRACTION	100
2.6509-2.7125	0.2568	305	0.2017	2802	X-RAY DIFFRACTION	100
2.7125-2.7804	0.2443	317	0.2037	2786	X-RAY DIFFRACTION	100
2.7804-2.8555	0.2374	301	0.2026	2833	X-RAY DIFFRACTION	100
2.8555-2.9395	0.2515	291	0.2024	2841	X-RAY DIFFRACTION	100
2.9395-3.0344	0.2235	339	0.196	2755	X-RAY DIFFRACTION	100
3.0344-3.1428	0.2209	317	0.1922	2794	X-RAY DIFFRACTION	100
3.1428-3.2687	0.2319	293	0.195	2842	X-RAY DIFFRACTION	100
3.2687-3.4174	0.2102	302	0.1924	2810	X-RAY DIFFRACTION	100
3.4174-3.5975	0.2018	296	0.1817	2810	X-RAY DIFFRACTION	100
3.5975-3.8228	0.1927	316	0.1636	2821	X-RAY DIFFRACTION	100
3.8228-4.1178	0.1649	299	0.1438	2862	X-RAY DIFFRACTION	100
4.1178-4.532	0.1651	348	0.1403	2778	X-RAY DIFFRACTION	100
4.532-5.1871	0.1557	299	0.1326	2828	X-RAY DIFFRACTION	100
5.1871-6.5327	0.205	330	0.1697	2834	X-RAY DIFFRACTION	100
6.5327-48.8733	0.1986	323	0.18	2855	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	1.1008	0.0498	-0.0195	2.1286	-0.5166	0.9276	-0.0913	0.1549	0.1619	-0.0341	0.0487	-0.0284	-0.2255	0.0815	0.0001	0.4034	-0.0436	-0.0246	0.342	0.015	0.2424	40.2816	5.154	17.1355
2	0.7482	0.0083	-0.0481	1.4784	-0.5251	1.0289	-0.0122	0.1486	0.0866	0.1482	0.1525	0.3946	-0.2894	-0.0807	0.0324	0.3927	0.0603	0.0518	0.2853	0.0324	0.4081	22.0936	-3.57	27.1663
3	0.3705	-0.3649	0.1772	0.7436	-0.6578	0.5608	-0.0624	0.0109	-0.0259	-0.0078	0.1417	0.2489	-0.2004	-0.1498	0.0001	0.4392	0.0225	0.0446	0.406	-0.0208	0.3613	31.7894	-14.1217	25.6705
4	2.9563	0.6432	0.1078	0.835	0.2389	1.2733	0.0297	-0.2279	-0.3176	0.0609	-0.0815	0.0131	-0.0082	-0.2666	-0.0001	0.2779	0.0023	-0.0175	0.3521	0.0545	0.2951	16.9376	14.0627	-12.6563
5	0.9028	-0.117	0.445	0.4404	-0.0201	0.7688	0.0115	0.274	-0.8763	-0.2868	-0.0323	-0.552	0.1479	0.1885	0.0358	0.3042	0.054	0.0314	0.2381	-0.0703	0.83	34.8188	-1.6056	-22.6057
6	2.2301	0.9281	-0.3585	0.583	0.2503	0.7385	-0.0362	0.0588	-0.5535	0.0421	-0.035	-0.1421	-0.0572	0.0592	-0.0018	0.2847	0.0349	-0.0153	0.2868	0.0329	0.4171	33.2614	11.6537	-20.2241
7	0.384	-0.1269	0.0828	0.1367	-0.135	0.2015	0.0222	0.1645	-0.113	0.0489	-0.0611	0.1814	0.1135	-0.7709	-0.0001	0.3447	-0.02	0.0121	0.4999	-0.0307	0.3755	-1.7375	-47.773	35.469
8	0.2579	-0.2038	0.2994	0.5666	0.09	0.6247	0.0082	-0.0415	0.0253	0.2523	-0.0103	0.2379	0.4396	-0.2099	-0.0003	0.4326	-0.0926	0.0359	0.3814	0.0493	0.3794	-0.4396	-56.3168	48.4728
9	0.542	0.1005	-0.2232	0.7904	-0.4131	0.8274	-0.0224	-0.1039	-0.1329	0.1809	-0.0007	-0.1075	0.3503	-0.1006	0.0001	0.4152	0.0023	-0.0288	0.3252	0.0396	0.3692	6.9561	-53.7715	45.8846
10	0.3692	0.2695	-0.1341	0.2068	-0.208	0.4487	0.0295	0.0718	0.1408	-0.1329	0.0166	-0.1809	0.2966	-0.3109	-0	0.3018	0.0224	-0.0263	0.3548	-0.0137	0.3306	4.6277	-44.2012	31.3209
11	0.9815	0.1367	-0.5817	1.1275	-0.4982	0.7496	0.1739	-0.1077	0.0038	0.192	-0.0334	-0.1896	-0.1494	0.1301	-0.0002	0.3097	0.0279	-0.0021	0.3399	-0.0059	0.3752	20.1071	-32.8554	39.0458
12	0.138	-0.5223	0.0327	2.2532	-0.3292	0.9557	0.166	0.122	0.3652	0.6827	0.4344	0.3351	-0.8399	-0.6234	0.9846	0.8343	0.2739	0.3925	0.5304	0.1293	0.6674	4.9283	-16.0388	47.7282
13	0.6736	0.7029	0.0335	1.3575	-0.6946	0.8649	0.0825	0.0227	0.2433	0.3482	0.1768	0.0884	-0.1379	-0.0922	0.0169	0.352	0.0727	0.0776	0.3454	0.0347	0.3988	11.0483	-26.9954	39.1477
14	0.2878	0.2419	-0.1033	0.1909	-0.0677	0.4261	0.0392	0.2038	-0.0713	-0.1415	-0.0311	-0.0271	0.0145	-0.1549	-0.0001	0.3646	0.095	-0.0005	0.3604	0.0209	0.4013	12.0936	-34.8115	28.8648
15	0.1057	0.1396	-0.0015	0.3359	0.1542	0.1249	0.0641	-0.1328	-0.2424	-0.039	0.0759	-0.0426	0.3598	0.195	0.0023	0.3456	0.0651	-0.0328	0.4668	0.0483	0.4617	29.2812	-33.681	34.1766

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID -2 THROUGH 233 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 234 THROUGH 349 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 350 THROUGH 385 )
4	X-RAY DIFFRACTION	4	CHAIN 'B' AND (RESID -2 THROUGH 233 )
5	X-RAY DIFFRACTION	5	CHAIN 'B' AND (RESID 234 THROUGH 317 )
6	X-RAY DIFFRACTION	6	CHAIN 'B' AND (RESID 318 THROUGH 386 )
7	X-RAY DIFFRACTION	7	CHAIN 'C' AND (RESID -2 THROUGH 24 )
8	X-RAY DIFFRACTION	8	CHAIN 'C' AND (RESID 25 THROUGH 65 )
9	X-RAY DIFFRACTION	9	CHAIN 'C' AND (RESID 66 THROUGH 143 )
10	X-RAY DIFFRACTION	10	CHAIN 'C' AND (RESID 144 THROUGH 176 )
11	X-RAY DIFFRACTION	11	CHAIN 'C' AND (RESID 177 THROUGH 252 )
12	X-RAY DIFFRACTION	12	CHAIN 'C' AND (RESID 253 THROUGH 276 )
13	X-RAY DIFFRACTION	13	CHAIN 'C' AND (RESID 277 THROUGH 340 )
14	X-RAY DIFFRACTION	14	CHAIN 'C' AND (RESID 341 THROUGH 368 )
15	X-RAY DIFFRACTION	15	CHAIN 'C' AND (RESID 369 THROUGH 385 )

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