PDB-5qcq: Crystal structure of BACE complex with BMC025

ID or keywords:

Entry

Database: PDB / ID: 5qcq

Title

Crystal structure of BACE complex with BMC025

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 / amyloid-beta metabolic process / prepulse inhibition ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.97 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	5qcq.cif.gz	457.2 KB	Display	PDBx/mmCIF format
PDB format	pdb5qcq.ent.gz	389.9 KB	Display	PDB format
PDBx/mmJSON format	5qcq.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5qcq_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	5qcq_full_validation.pdf.gz	1.1 MB	Display
Data in XML	5qcq_validation.xml.gz	45.6 KB	Display
Data in CIF	5qcq_validation.cif.gz	66.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qc/5qcq ftp://data.pdbj.org/pub/pdb/validation_reports/qc/5qcq	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	3duy-1 3i25-1 3msj-2 3uqx-d 5dqc-2 5qd1-1 4dv9-d 3uqu-d 6nv7-1 3ixj-3 4fco-d 5qd0-2 3ivi-3 3ckp-3 4fhp-d 4j1i-d 3ckr-1 3ufl-d 4i0h-3 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)	82.537, 103.062, 100.602
Angle α, β, γ (deg.)	90.00, 103.64, 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 156 OR RESID 169 THROUGH 385))
2	1	1	(CHAIN B AND (RESID -2 THROUGH 309 OR RESID 317 THROUGH 385))
3	1	1	(CHAIN C AND (RESID -2 THROUGH 156 OR RESID 169 THROUGH 309 OR RESID 317 THROUGH 385))

#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-AFJ / (2R,4S,5S)-N-butyl-4-hydroxy-2,7-dimethyl-5-{[N-(4-methylpentanoyl)-L-methionyl]amino}octanamide / (2R,4S,5S)-4-Hydroxy-2,7-dimethyl-5-[(S)-2-(4-methyl-pentanoylamino)-4-methylsulfanyl-butyrylamino]-octanoic acid butylamide Mass: 487.739 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂₅H₄₉N₃O₄S
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 639 / 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: 3.1 Å³/Da / Density % sol: 60.26 %
Crystal grow	Temperature: 292 K / Method: hanging drop Details: CRYSTALS WERE GROWN AT 19C BY VAPOUR DIFFUSION IN HANGING DROPS FROM 1.0M AMMONIUM SULFATE IN WATER. PROTEIN STOCK WAS BACE MUT46B BATCH XII 8.5MG/ML IN 10MM TRIS-HCL PH 7.4, 25MM NACL, WITH ...Details: CRYSTALS WERE GROWN AT 19C BY VAPOUR DIFFUSION IN HANGING DROPS FROM 1.0M AMMONIUM SULFATE IN WATER. PROTEIN STOCK WAS BACE MUT46B BATCH XII 8.5MG/ML IN 10MM TRIS-HCL PH 7.4, 25MM NACL, WITH A 5-FOLD EXCESS OF BMC025 ADDED FROM A 50MM STOCK SOLUTION IN 90% DMSO-D6 (1.8% DMSO IN DROP). A SOLUTION CONTAINING 1.2M AMMONIUM SULFATE, 25% GLYCEROL, 1MM BMC025 AND 1.8% DMSO WAS USED AS CRYO-PROTECTANT.

Crystal

Density Matthews: 3.1 Å³/Da / Density % sol: 60.26 %

Crystal grow

Temperature: 292 K / Method: hanging drop
Details: CRYSTALS WERE GROWN AT 19C BY VAPOUR DIFFUSION IN HANGING DROPS FROM 1.0M AMMONIUM SULFATE IN WATER. PROTEIN STOCK WAS BACE MUT46B BATCH XII 8.5MG/ML IN 10MM TRIS-HCL PH 7.4, 25MM NACL, WITH ...

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.54178
Detector	Type: RIGAKU SATURN 92 / Detector: CCD / Date: Nov 18, 2005
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54178 Å / Relative weight: 1
Reflection	Resolution: 1.971→48.882 Å / Num. obs: 107921 / % possible obs: 93.5 % / R_merge(I) obs: 0.061

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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
XSCALE		data scaling
XDS		date reduction
PDB_EXTRACT	3.24	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.97→48.88 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 18.84 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.195	10413	9.65 %
R_work	0.167	-	-
obs	0.17	107921	93.5 %

Solvent computation

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

Displacement parameters

B_iso mean: 39.15 Å²

Refinement step

Cycle: LAST / Resolution: 1.97→48.88 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8777	0	99	639	9515

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	9107
X-RAY DIFFRACTION	f_angle_d	0.845	12366
X-RAY DIFFRACTION	f_dihedral_angle_d	15.088	5315
X-RAY DIFFRACTION	f_chiral_restr	0.06	1341
X-RAY DIFFRACTION	f_plane_restr	0.005	1585

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type
1	1	A	5310	X-RAY DIFFRACTION	POSITIONAL
1	2	B	5310	X-RAY DIFFRACTION	POSITIONAL
1	3	C	5310	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 (%)
1.9706-1.993	0.3042	113	0.2492	2005	X-RAY DIFFRACTION	56
1.993-2.0164	0.276	139	0.2534	2316	X-RAY DIFFRACTION	64
2.0164-2.041	0.2697	138	0.2384	2445	X-RAY DIFFRACTION	68
2.041-2.0669	0.2891	222	0.2297	2695	X-RAY DIFFRACTION	75
2.0669-2.0941	0.2601	328	0.2171	2758	X-RAY DIFFRACTION	81
2.0941-2.1227	0.2504	336	0.2093	2958	X-RAY DIFFRACTION	86
2.1227-2.1531	0.2446	361	0.1951	3246	X-RAY DIFFRACTION	93
2.1531-2.1852	0.2196	357	0.1829	3443	X-RAY DIFFRACTION	100
2.1852-2.2194	0.2357	379	0.1799	3456	X-RAY DIFFRACTION	100
2.2194-2.2557	0.2146	397	0.182	3433	X-RAY DIFFRACTION	100
2.2557-2.2946	0.2128	399	0.1778	3441	X-RAY DIFFRACTION	100
2.2946-2.3364	0.2239	396	0.1787	3456	X-RAY DIFFRACTION	100
2.3364-2.3813	0.2364	354	0.173	3430	X-RAY DIFFRACTION	100
2.3813-2.4299	0.2248	389	0.1745	3508	X-RAY DIFFRACTION	100
2.4299-2.4827	0.2157	420	0.1796	3407	X-RAY DIFFRACTION	100
2.4827-2.5405	0.1948	361	0.1687	3470	X-RAY DIFFRACTION	100
2.5405-2.604	0.2205	395	0.1639	3449	X-RAY DIFFRACTION	100
2.604-2.6744	0.2012	395	0.1703	3421	X-RAY DIFFRACTION	100
2.6744-2.7531	0.1897	384	0.173	3488	X-RAY DIFFRACTION	100
2.7531-2.842	0.2043	397	0.1757	3429	X-RAY DIFFRACTION	100
2.842-2.9435	0.1909	362	0.1678	3530	X-RAY DIFFRACTION	100
2.9435-3.0614	0.1896	389	0.1637	3443	X-RAY DIFFRACTION	100
3.0614-3.2007	0.2106	363	0.1654	3465	X-RAY DIFFRACTION	100
3.2007-3.3694	0.2091	362	0.1677	3500	X-RAY DIFFRACTION	100
3.3694-3.5804	0.1764	394	0.1542	3491	X-RAY DIFFRACTION	100
3.5804-3.8568	0.1702	377	0.1465	3445	X-RAY DIFFRACTION	100
3.8568-4.2447	0.1556	388	0.1373	3482	X-RAY DIFFRACTION	100
4.2447-4.8584	0.1487	394	0.1295	3426	X-RAY DIFFRACTION	99
4.8584-6.1192	0.1909	413	0.1568	3428	X-RAY DIFFRACTION	99
6.1192-48.8974	0.1989	311	0.202	3044	X-RAY DIFFRACTION	85

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	0.5122	-0.0472	0.0651	0.1834	-0.1533	0.1823	-0.2599	-0.3015	0.5285	0.2649	0.1015	-0.1644	-0.3823	0.0772	-0.1657	0.3485	-0.028	-0.0965	0.2161	-0.0223	0.2653	44.7867	9.6369	26.9481
2	0.1198	-0.0657	-0.0147	0.0428	-0.0039	0.2145	0.0096	0.1564	0.4051	-0.0522	-0.0491	-0.1844	-0.1713	0.0024	-0.0004	0.3891	-0.0746	-0.0531	0.1995	0.0371	0.3528	40.4152	16.8509	17.1886
3	0.3032	0.0283	-0.2639	0.5983	0.026	0.5353	-0.0491	0.2324	0.4548	-0.1036	-0.0267	-0.0523	-0.6465	-0.085	-0.0767	0.3419	-0.1258	-0.0282	0.2116	0.1015	0.2315	42.9702	15.0999	12.1312
4	0.6008	-0.0509	0.1632	1.1771	-0.1144	0.3174	-0.0724	0.0986	0.0413	-0.0399	0.0328	-0.1452	-0.0627	0.0969	-0.0001	0.2527	-0.0345	0.0103	0.2114	-0.014	0.1272	43.6189	-2.5251	18.0335
5	0.8926	-0.3235	-0.0245	0.4309	-0.0224	0.526	-0.122	0.2562	-0.0671	-0.1648	0.2611	0.5599	-0.1643	-0.2032	0.0999	0.1846	0.0633	-0.0076	0.2054	0.0862	0.3533	18.1322	-6.7049	21.9028
6	0.5921	0.2319	0.2673	0.477	-0.2001	0.4129	-0.0353	0.1212	-0.0461	0.1174	0.0376	0.3304	-0.1362	-0.1409	0.0158	0.2471	0.051	0.065	0.1707	0.0249	0.2137	24.0394	-6.3177	28.0027
7	0.483	-0.012	0.2166	0.7992	-0.4499	0.4892	-0.0434	0.0075	-0.1139	0.0762	0.1133	0.1205	-0.1323	-0.0922	0.0032	0.2449	0.0392	0.0269	0.1983	0.0006	0.1571	34.0744	-11.8544	25.1753
8	1.956	0.5213	0.2212	0.8698	0.2254	1.4445	0.0315	-0.2049	-0.224	0.0694	-0.073	0.0347	0.0424	-0.2737	-0.0063	0.1523	0.0063	-0.0093	0.2074	0.0528	0.1655	17.0766	13.927	-12.6525
9	0.89	0.0424	0.1727	0.4862	0.0018	0.8795	-0.172	0.4705	-1.0042	-0.2859	0.0849	-0.7121	0.3246	0.312	-0.3165	0.2652	0.105	0.09	0.0483	-0.1264	0.7515	34.1595	-0.7139	-23.3886
10	0.745	0.3755	-0.1262	0.4291	0.2937	0.6035	-0.0452	0.082	-0.3442	0.0386	0.0226	-0.1069	0.0071	0.2012	-0.0114	0.1796	0.0337	-0.0211	0.1992	0.0487	0.2776	35.7005	14.8419	-18.9299
11	0.3073	-0.1718	-0.2968	0.2662	0.0397	0.5063	0.0755	0.1071	-0.0704	0.0494	-0.0314	0.0971	0.1529	-0.7501	-0.0628	0.199	-0.0347	0.0155	0.3602	0.0028	0.2569	-1.8792	-48.0412	35.6968
12	0.1646	0.0935	-0.0821	0.3559	-0.0572	0.5635	0.0454	-0.2154	-0.0397	0.223	-0.1022	0.0692	0.2531	-0.1343	-0.0038	0.2785	-0.0701	0.0126	0.3015	0.1072	0.2748	1.3061	-55.0961	49.7686
13	0.9547	0.3605	-0.198	0.7298	-0.3752	0.9612	-0.0597	-0.0517	-0.1912	-0.0165	-0.0099	-0.0657	0.263	-0.1954	-0.0151	0.214	0.015	-0.0109	0.2015	0.0652	0.2636	6.3814	-52.2831	40.5913
14	0.9489	0.136	-0.3687	0.9938	-0.3018	0.6719	0.1927	-0.2019	0.0084	0.2698	-0.053	-0.043	-0.1341	0.07	0.1098	0.1961	0.0089	0.0422	0.2194	0.0123	0.1761	17.8184	-28.8446	42.5199
15	0.259	0.3664	-0.0131	0.7488	-0.1203	0.4223	0.1737	-0.0086	0.1834	0.1519	0.0368	0.0457	-0.1135	-0.0689	0.0673	0.1975	0.0593	0.0815	0.229	0.0547	0.2461	11.7109	-26.3911	38.7435
16	0.4566	0.3013	-0.513	0.3978	-0.1337	0.6251	0.077	0.0813	-0.0062	0.1036	-0.0093	-0.0429	-0.0901	0.0087	0.0111	0.186	0.0631	0.0078	0.1804	0.0464	0.2281	17.3942	-34.6777	31.4606

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID -2 THROUGH 24 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 25 THROUGH 53 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 54 THROUGH 116 )
4	X-RAY DIFFRACTION	4	CHAIN 'A' AND (RESID 117 THROUGH 202 )
5	X-RAY DIFFRACTION	5	CHAIN 'A' AND (RESID 203 THROUGH 270 )
6	X-RAY DIFFRACTION	6	CHAIN 'A' AND (RESID 271 THROUGH 334 )
7	X-RAY DIFFRACTION	7	CHAIN 'A' AND (RESID 335 THROUGH 385 )
8	X-RAY DIFFRACTION	8	CHAIN 'B' AND (RESID -2 THROUGH 233 )
9	X-RAY DIFFRACTION	9	CHAIN 'B' AND (RESID 234 THROUGH 334 )
10	X-RAY DIFFRACTION	10	CHAIN 'B' AND (RESID 335 THROUGH 385 )
11	X-RAY DIFFRACTION	11	CHAIN 'C' AND (RESID -2 THROUGH 24 )
12	X-RAY DIFFRACTION	12	CHAIN 'C' AND (RESID 25 THROUGH 74 )
13	X-RAY DIFFRACTION	13	CHAIN 'C' AND (RESID 75 THROUGH 183 )
14	X-RAY DIFFRACTION	14	CHAIN 'C' AND (RESID 184 THROUGH 271 )
15	X-RAY DIFFRACTION	15	CHAIN 'C' AND (RESID 272 THROUGH 334 )
16	X-RAY DIFFRACTION	16	CHAIN 'C' AND (RESID 335 THROUGH 385 )

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