PDB-5qdb: Crystal structure of BACE complex with BMC002

ID or keywords:

Entry

Database: PDB / ID: 5qdb

Title

Crystal structure of BACE complex with BMC002

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 / cellular response to manganese ion /

prepulse inhibition / amyloid-beta metabolic process ...
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: Derived calculations / Structure summary Category: audit_author / chem_comp ...audit_author / chem_comp / entity / pdbx_entity_nonpoly Item: _audit_author.identifier_ORCID / _chem_comp.name ..._audit_author.identifier_ORCID / _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name
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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PDBx/mmCIF format	5qdb.cif.gz	455.6 KB	Display	PDBx/mmCIF format
PDB format	pdb5qdb.ent.gz	388.8 KB	Display	PDB format
PDBx/mmJSON format	5qdb.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qd/5qdb ftp://data.pdbj.org/pub/pdb/validation_reports/qd/5qdb	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	5qd5-2 5qd6-1 4d8c-3 5qcp-2 6lyj-1 3pi5-3 2qzk-d 3i25-3 5clm-d 5qd9-1 5qd6-2 4cdd-1 3skg-4 5qcx-1 2p83-3 5dqc-3 4zpg-d 3qbh-3 5qd4-2 3k5f-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
45.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Beta-secretase 1

hetero molecules

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

3

C: Beta-secretase 1

hetero molecules

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

Unit cell

Length a, b, c (Å)	81.661, 103.353, 99.474
Angle α, β, γ (deg.)	90.00, 103.72, 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 AND (RESID -2 THROUGH 157 OR RESID 169 THROUGH 385))

#1: Protein	Beta-secretase 1 / Mass: 44777.336 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P56817
#2: Chemical	ChemComp-BAV / (3S,14R,16S)-16-[(1R)-1-hydroxy-2-{[3-(1-methylethyl)benzyl]amino}ethyl]-3,4,14-trimethyl-1,4-diazacyclohexadecane-2,5- dione / (3S,14R,16S)-16-[(R)-1-Hydroxy-2-(3-isopropyl-benzylamino)-ethyl]-3,4,14-trimethyl-1,4diaza-cyclohexadecane-2,5-dione Mass: 487.718 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂₉H₄₉N₃O₃
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 292 / 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: 3.04 Å³/Da / Density % sol: 59.48 %
Crystal grow	Temperature: 292 K / Method: hanging drop / pH: 5.1 Details: CRYSTALS WERE GROWN AT 19C BY VAPOUR DIFFUSION IN HANGING DROPS USING 1.0M AMMONIUM PHOSPHATE, 0.1M NA CITRATE PH 5.1 AS PRECIPITANT. PROTEIN STOCK WAS BACE MUT46B BATCH XII 8.45MG/ML IN ...Details: CRYSTALS WERE GROWN AT 19C BY VAPOUR DIFFUSION IN HANGING DROPS USING 1.0M AMMONIUM PHOSPHATE, 0.1M NA CITRATE PH 5.1 AS PRECIPITANT. PROTEIN STOCK WAS BACE MUT46B BATCH XII 8.45MG/ML IN 10MM TRIS-HCL PH 7.4,25MM NACL, WITH A 3.8-FOLD EXCESS OF BMC002 ADDED FROM A 50MM STOCK SOLUTION IN DMSO (1.4% DMSO IN DROP). CRYO-PROTECTANT WAS 20% (V/V) 1,2-PROPANEDIOL, 80% RESERVOIR SOLUTION.

Crystal

Density Matthews: 3.04 Å³/Da / Density % sol: 59.48 %

Crystal grow

Temperature: 292 K / Method: hanging drop / pH: 5.1
Details: CRYSTALS WERE GROWN AT 19C BY VAPOUR DIFFUSION IN HANGING DROPS USING 1.0M AMMONIUM PHOSPHATE, 0.1M NA CITRATE PH 5.1 AS PRECIPITANT. PROTEIN STOCK WAS BACE MUT46B BATCH XII 8.45MG/ML IN ...

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Data collection

Diffraction	Mean temperature: 96 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97933
Detector	Type: MAR CCD 165 mm / Detector: CCD / Date: Apr 15, 2004
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97933 Å / Relative weight: 1
Reflection	Resolution: 2.1→48.71 Å / Num. obs: 93593 / % possible obs: 100 % / R_merge(I) obs: 0.068

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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→48.71 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 19.27 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.192	9359	10 %
R_work	0.167	-	-
obs	0.17	93593	100 %

Solvent computation

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

Displacement parameters

B_iso mean: 53.75 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→48.71 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8925	0	105	292	9322

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	9272
X-RAY DIFFRACTION	f_angle_d	0.9	12604
X-RAY DIFFRACTION	f_dihedral_angle_d	14.849	5421
X-RAY DIFFRACTION	f_chiral_restr	0.061	1368
X-RAY DIFFRACTION	f_plane_restr	0.006	1617

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type
1	1	A	5417	X-RAY DIFFRACTION	POSITIONAL
1	2	B	5417	X-RAY DIFFRACTION	POSITIONAL
1	3	C	5417	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 (%)
2.1-2.1239	0.2276	276	0.196	2836	X-RAY DIFFRACTION	100
2.1239-2.1489	0.2309	300	0.1935	2795	X-RAY DIFFRACTION	100
2.1489-2.1751	0.2356	306	0.188	2803	X-RAY DIFFRACTION	100
2.1751-2.2026	0.219	291	0.1878	2836	X-RAY DIFFRACTION	100
2.2026-2.2316	0.2174	309	0.1773	2777	X-RAY DIFFRACTION	100
2.2316-2.2622	0.2278	303	0.182	2806	X-RAY DIFFRACTION	100
2.2622-2.2945	0.2327	337	0.1912	2743	X-RAY DIFFRACTION	100
2.2945-2.3287	0.2177	320	0.1883	2809	X-RAY DIFFRACTION	100
2.3287-2.3651	0.2384	332	0.1883	2760	X-RAY DIFFRACTION	100
2.3651-2.4039	0.2281	316	0.1857	2805	X-RAY DIFFRACTION	100
2.4039-2.4453	0.21	301	0.1798	2790	X-RAY DIFFRACTION	100
2.4453-2.4898	0.2295	344	0.1793	2791	X-RAY DIFFRACTION	100
2.4898-2.5377	0.2029	319	0.1746	2777	X-RAY DIFFRACTION	100
2.5377-2.5895	0.2194	311	0.178	2818	X-RAY DIFFRACTION	100
2.5895-2.6458	0.2184	301	0.1897	2830	X-RAY DIFFRACTION	100
2.6458-2.7073	0.2189	293	0.1897	2811	X-RAY DIFFRACTION	100
2.7073-2.775	0.2313	307	0.1952	2772	X-RAY DIFFRACTION	100
2.775-2.8501	0.2395	322	0.1949	2814	X-RAY DIFFRACTION	100
2.8501-2.9339	0.2278	330	0.1904	2800	X-RAY DIFFRACTION	100
2.9339-3.0286	0.2221	304	0.1866	2820	X-RAY DIFFRACTION	100
3.0286-3.1368	0.229	339	0.1891	2779	X-RAY DIFFRACTION	100
3.1368-3.2624	0.2287	299	0.1917	2825	X-RAY DIFFRACTION	100
3.2624-3.4108	0.1977	319	0.1856	2804	X-RAY DIFFRACTION	100
3.4108-3.5906	0.1908	301	0.1714	2799	X-RAY DIFFRACTION	100
3.5906-3.8155	0.1807	329	0.1574	2797	X-RAY DIFFRACTION	100
3.8155-4.1099	0.1672	301	0.1379	2854	X-RAY DIFFRACTION	100
4.1099-4.5233	0.1492	325	0.1356	2812	X-RAY DIFFRACTION	100
4.5233-5.1772	0.141	324	0.1283	2811	X-RAY DIFFRACTION	100
5.1772-6.5202	0.1734	290	0.1629	2871	X-RAY DIFFRACTION	100
6.5202-48.7227	0.1863	310	0.1728	2889	X-RAY DIFFRACTION	100

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	0.7096	0.0303	-0.1097	1.4244	-0.4545	0.9231	-0.0688	0.1265	0.1311	0.0534	0.042	-0.0275	-0.1319	0.0884	0	0.3781	0.0091	-0.0247	0.3876	0.0092	0.3211	39.8326	5.0953	16.8612
2	1.262	0.3345	0.001	1.3584	-0.607	0.9128	-0.0345	0.0796	0.1941	0.2883	0.1588	0.3202	-0.1863	-0.0888	0.0012	0.4004	0.0811	0.0677	0.343	0.0233	0.4128	20.1076	-3.6687	27.1951
3	0.7141	-0.1496	0.07	0.9706	-0.5566	0.5486	0.019	0.1304	-0.0602	0.1295	0.0565	0.0157	0.0444	-0.1057	-0.0001	0.379	0.0367	0.0399	0.3652	-0.0336	0.3182	34.3745	-12.9617	24.3199
4	2.2844	0.6887	-0.1383	0.974	0.0541	1.6387	-0.004	-0.1106	-0.2087	0.0031	-0.0553	0.0298	-0.0079	-0.3051	-0.0003	0.3366	-0.0024	-0.0223	0.3689	0.0327	0.3401	16.2632	13.8507	-12.3807
5	1.6829	0.1385	0.4369	0.4781	0.017	1.2876	0.0174	0.1817	-0.6922	-0.2207	-0.0169	-0.3753	0.3172	0.1351	-0.0008	0.4343	0.0365	0.0475	0.2528	-0.081	0.6665	33.9156	-1.5095	-22.3016
6	2.1782	0.8678	0.2502	0.2848	0.0381	1.1706	0.0149	0.1246	-0.5024	-0.0148	-0.0092	-0.1912	0.0582	0.0432	0.0012	0.3919	-0.0065	-0.0067	0.3144	0.0326	0.4794	32.7125	11.6356	-19.6429
7	0.3743	-0.2078	-0.1763	1.0215	-0.2072	0.5993	0.0174	0.1249	-0.0155	0.0351	-0.0454	0.2839	0.0831	-0.3775	0.0001	0.3655	-0.0108	-0.0067	0.5058	-0.0048	0.4831	-0.8602	-50.2688	41.6884
8	1.1827	0.4692	-0.4211	1.4591	-0.1727	1.8058	0.0123	-0.0251	-0.169	0.0361	-0.0414	-0.0177	0.3075	-0.1559	0.0001	0.3753	-0.0074	-0.0269	0.3497	0.0307	0.4018	6.5446	-54.2712	43.9358
9	0.7198	-0.1682	-0.5555	1.3739	-0.3977	1.3272	0.1591	-0.0497	0.0314	0.2526	0.0073	-0.0693	-0.1544	0.0227	0.0003	0.3702	0.0374	0.02	0.3651	0.0041	0.3821	15.7475	-29.4262	40.0313
10	0.5749	0.5969	0.1045	1.3185	-0.5871	0.9145	0.0963	-0.0048	0.0984	0.1423	0.0199	0.2036	-0.0266	-0.1432	0.0013	0.3321	0.0525	0.0328	0.4075	0.0178	0.4022	11.8132	-30.3668	37.9498
11	0.4875	0.5399	-0.5216	0.6304	-0.2142	0.7739	0.0328	0.1384	0.0469	-0.0277	-0.0894	0.0035	-0.1965	0.1262	-0	0.3645	0.0779	-0.0198	0.3603	-0.0004	0.4204	19.6768	-33.7389	30.6229

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 340 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 341 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 385 )
7	X-RAY DIFFRACTION	7	CHAIN 'C' AND (RESID -2 THROUGH 53 )
8	X-RAY DIFFRACTION	8	CHAIN 'C' AND (RESID 54 THROUGH 169 )
9	X-RAY DIFFRACTION	9	CHAIN 'C' AND (RESID 170 THROUGH 282 )
10	X-RAY DIFFRACTION	10	CHAIN 'C' AND (RESID 283 THROUGH 346 )
11	X-RAY DIFFRACTION	11	CHAIN 'C' AND (RESID 347 THROUGH 385 )

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