PDB-4hkz: Trastuzumab Fab complexed with Protein L and Protein A fragments

ID or keywords:

Entry

Database: PDB / ID: 4hkz

Title

Trastuzumab Fab complexed with Protein L and Protein A fragments

Components

Immunoglobulin G-binding protein A
Protein L fragment
Trastuzumab heavy chain
Trastuzumab light chain

Keywords

IMMUNE SYSTEM / monoclonal antibody / cancer therapeutic

Function / homology

Function and homology information

IgG binding / immunoglobulin binding / extracellular region
Similarity search - Function

Biological species

Homo sapiens (human)

Staphylococcus aureus (bacteria)

FINEGOLDIA MAGNA (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.08 Å

Authors

Avery, K.N. / Zer, C. / Bzymek, K.P. / Williams, J.C.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Identification and grafting of a unique peptide-binding site in the Fab framework of monoclonal antibodies.
Authors: Donaldson, J.M. / Zer, C. / Avery, K.N. / Bzymek, K.P. / Horne, D.A. / Williams, J.C.

History

Deposition	Oct 15, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 9, 2013	Provider: repository / Type: Initial release
Revision 1.1	Oct 23, 2013	Group: Database references
Revision 1.2	Nov 6, 2013	Group: Database references
Revision 1.3	Nov 15, 2017	Group: Refinement description / Category: software / Item: _software.name

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4hkz.cif.gz	237.3 KB	Display	PDBx/mmCIF format
PDB format	pdb4hkz.ent.gz	198.5 KB	Display	PDB format
PDBx/mmJSON format	4hkz.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4hkz_validation.pdf.gz	436.3 KB	Display	wwPDB validaton report
Full document	4hkz_full_validation.pdf.gz	438.3 KB	Display
Data in XML	4hkz_validation.xml.gz	27.3 KB	Display
Data in CIF	4hkz_validation.cif.gz	40.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hk/4hkz ftp://data.pdbj.org/pub/pdb/validation_reports/hk/4hkz	HTTPS FTP

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Related structure data

Related structure data	4gw1C 4gw5C 4hjgC 4ioiC 1n8z C: citing same article (ref.)
Similar structure data	4hjg-d 6b9z-d 4ioi-d 5u5f-d 6o28-1 6bah-d 5u5m-d 6bae-d 6nt2-2 5u6a-d 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
Related items in Molecule of the Month	#256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1) #21 - Sep 2001 Antibodies similarity (1) #211 - Jul 2017 Pilus Machine similarity (4)

Deposited unit

A: Trastuzumab light chain

B: Trastuzumab heavy chain

H: Immunoglobulin G-binding protein A

E: Protein L fragment

hetero molecules

59.8 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	53.520, 104.670, 117.550
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Protein , 1 types, 1 molecules E

#4: Protein	Protein L fragment Mass: 6850.605 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) FINEGOLDIA MAGNA (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q51918*PLUS

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Antibody , 3 types, 3 molecules ABH

#1: Antibody	Trastuzumab light chain Mass: 23362.889 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Mus musculus (house mouse)
#2: Antibody	Trastuzumab heavy chain Mass: 23554.359 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Mus musculus (house mouse)
#3: Antibody	Immunoglobulin G-binding protein A / IgG-binding protein A / Staphylococcal protein A Mass: 6037.530 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: Mu50 / ATCC 700699 / Gene: spa, SAV0111 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A015

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Non-polymers , 2 types, 558 molecules

#5: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 557 / 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: 2.75 Å³/Da / Density % sol: 55.32 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 50 mM Hepes, 20% PEG 3350, 100 mM NaCl, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837 Å
Detector	Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 26, 2011
Radiation	Monochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.91837 Å / Relative weight: 1
Reflection	Resolution: 2.08→47.81 Å / Num. all: 40478 / Num. obs: 40077 / % possible obs: 99 % / Observed criterion σ(F): 1.36 / Observed criterion σ(I): 2 / Redundancy: 4.2 % / R_merge(I) obs: 0.067 / Net I/σ(I): 14.4
Reflection shell	Resolution: 2.08→2.13 Å / Redundancy: 3.2 % / R_merge(I) obs: 0.395 / Mean I/σ(I) obs: 3.1 / % possible all: 92.3

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Processing

Software

Name	Version	Classification
Blu-Ice		data collection
MOLREP		phasing
PHENIX	(phenix.refine: 1.8.1_1168)	refinement
XDS		data reduction
XSCALE		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.08→47.81 Å / SU ML: 0.21 / σ(F): 1.36 / Phase error: 21.26 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2065	2003	5 %	random
R_work	0.162	-	-	-
obs	0.1643	40076	99.02 %	-
all	-	40478	-	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.08→47.81 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4200	0	1	557	4758

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	4422
X-RAY DIFFRACTION	f_angle_d	1.066	6030
X-RAY DIFFRACTION	f_dihedral_angle_d	13.459	1628
X-RAY DIFFRACTION	f_chiral_restr	0.078	674
X-RAY DIFFRACTION	f_plane_restr	0.005	787

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 (%)
2.08-2.132	0.2626	130	0.2207	2485	X-RAY DIFFRACTION	92
2.132-2.1896	0.2556	140	0.2026	2645	X-RAY DIFFRACTION	98
2.1896-2.2541	0.2442	140	0.1994	2688	X-RAY DIFFRACTION	100
2.2541-2.3268	0.2666	142	0.1923	2701	X-RAY DIFFRACTION	100
2.3268-2.41	0.2234	143	0.1872	2721	X-RAY DIFFRACTION	100
2.41-2.5065	0.2717	143	0.1884	2703	X-RAY DIFFRACTION	100
2.5065-2.6205	0.2546	143	0.1842	2712	X-RAY DIFFRACTION	100
2.6205-2.7587	0.2485	142	0.1808	2709	X-RAY DIFFRACTION	99
2.7587-2.9315	0.2212	144	0.1763	2740	X-RAY DIFFRACTION	100
2.9315-3.1578	0.2158	145	0.1737	2751	X-RAY DIFFRACTION	100
3.1578-3.4755	0.1934	144	0.153	2731	X-RAY DIFFRACTION	100
3.4755-3.9782	0.1754	144	0.1399	2747	X-RAY DIFFRACTION	100
3.9782-5.0113	0.1434	148	0.1162	2813	X-RAY DIFFRACTION	100
5.0113-47.8233	0.2039	155	0.1625	2927	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	0.5262	0.6263	-0.6339	1.473	-1.4221	3.1794	-0.0015	0.0197	-0.0711	0.0463	-0.0139	-0.0242	0.071	0.115	0.0131	0.0654	0.0264	0.0053	0.1241	-0.0173	0.1305	-14.7556	-30.5278	11.3986
2	1.8352	-1.4327	-0.774	4.1076	0.6322	3.1121	0.0777	-0.1152	0.1129	0.4466	0.2091	0.5077	-0.4153	-0.3402	-0.2602	0.3328	0.0288	0.0969	0.2339	0.0621	0.2184	-32.8511	-27.8818	42.3286
3	9.886	1.2728	-2.3147	1.1216	0.6764	3.8454	-0.498	-1.1027	-0.2284	0.5656	0.4003	-0.057	-0.1583	0.159	0.1451	0.2293	0.0066	-0.0174	0.0661	-0.024	0.1484	-18.6491	-4.8008	18.3059
4	4.794	-4.7735	-1.6491	5.1778	2.7744	3.2415	0.0363	-0.1835	0.261	0.0222	0.0868	-0.2998	-0.2855	0.3645	-0.1542	0.1525	-0.0701	-0.0061	0.1087	-0.0018	0.19	-8.5537	-4.0041	11.1736
5	2.6492	-0.7469	-0.8549	3.7082	-0.7327	3.4983	0.0364	0.1191	0.0838	-0.1121	-0.0511	0.0443	-0.183	-0.0461	0.0264	0.1076	0.0174	-0.0016	0.0998	-0.0333	0.0882	-17.5571	-6.9622	6.3592
6	1.9162	-2.5897	-1.3448	4.4033	0.366	2.7653	-0.1217	0.1482	-0.3259	0.2231	0.0627	0.4448	-0.0352	-0.1247	0.0619	0.0942	-0.0215	-0.0102	0.1052	-0.0105	0.1312	-22.0292	-9.5131	12.2132
7	0.2636	0.4438	-0.2953	1.1613	-1.3979	3.2475	0.0928	-0.1243	-0.0229	0.5328	-0.0113	-0.02	-0.4388	-0.026	-0.0723	0.3681	-0.0089	-0.0038	0.1485	0.011	0.1925	-21.6064	-16.5549	34.0382
8	3.3292	-1.9767	2.6686	1.1941	-1.8714	5.5837	0.0886	-0.221	0.4123	1.1306	-0.1941	-0.5256	-0.7204	0.0484	0.1813	0.7907	-0.0964	-0.1152	0.2527	-0.0225	0.2395	-18.861	-11.3331	44.8992
9	6.2526	2.5404	0.9941	2.2252	0.4442	1.0816	0.0807	1.7827	0.1017	-1.0165	-0.3471	-0.4611	-0.6272	0.8467	0.2715	0.824	0.3237	0.0668	0.9347	0.1215	0.5126	-21.0872	13.048	-4.4108
10	2.0016	-0.2608	-7.4776	7.9245	3.5226	7.8757	-0.0885	1.1402	0.583	-1.6149	-0.7377	-0.4126	0.1872	0.353	0.7449	0.5381	0.1085	0.0099	0.3065	0.0882	0.2389	-29.4939	13.5393	1.1412
11	5.8175	-2.0393	0.019	2.1468	-0.3081	2.6562	0.1214	0.1653	0.128	-0.2286	-0.1935	0.2665	-0.4675	-0.2232	0.0374	0.2641	0.0587	-0.0257	0.1281	-0.0269	0.1522	-31.2183	9.7792	8.931
12	2.0131	-0.2246	1.9778	2.8509	0.3197	5.2767	-0.0521	0.6669	0.375	-0.7598	-0.2342	0.0849	-0.2358	0.0873	0.2814	0.3061	0.0648	-0.0121	0.1952	0.0084	0.1509	-24.7449	3.0486	0.2564
13	9.1933	0.8573	-7.5409	3.5433	-1.0872	9.1918	0.493	0.507	-0.3642	-0.8058	-0.2744	1.0787	-0.0705	-1.0172	-0.2338	0.2453	0.0912	-0.1296	0.3165	-0.1072	0.3706	-39.1177	4.5301	4.7835
14	7.6027	-5.5132	1.9142	8.684	-1.3111	5.7061	-0.1732	-0.5945	-0.1648	0.6552	0.362	-0.2262	0.3424	-0.1959	-0.172	0.2674	-0.0515	-0.0541	0.1639	0.0102	0.2683	-25.9964	-43.8883	15.2841
15	7.0262	-2.0499	4.5992	4.3814	-1.1648	5.5888	0.2763	0.3309	-0.267	-0.1707	-0.0868	0.1901	0.3355	0.0721	-0.1294	0.0967	-0.0274	0.0094	0.1332	-0.0154	0.1946	-25.6501	-41.1576	8.3428
16	9.1859	-7.1357	-1.1141	9.9417	0.4563	8.6978	0.0454	0.0114	-1.2352	0.5664	0.2875	0.3484	1.3099	-0.5168	-0.3306	0.4936	-0.1002	-0.1511	0.2524	-0.0323	0.4445	-27.768	-50.0598	11.2964

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A AND (RESID 1:113)
2	X-RAY DIFFRACTION	2	CHAIN A AND (RESID 114:213)
3	X-RAY DIFFRACTION	3	CHAIN B AND (RESID 1:17)
4	X-RAY DIFFRACTION	4	CHAIN B AND (RESID 18:32)
5	X-RAY DIFFRACTION	5	CHAIN B AND (RESID 33:83)
6	X-RAY DIFFRACTION	6	CHAIN B AND (RESID 84:99)
7	X-RAY DIFFRACTION	7	CHAIN B AND (RESID 100:195)
8	X-RAY DIFFRACTION	8	CHAIN B AND (RESID 196:221)
9	X-RAY DIFFRACTION	9	CHAIN H AND (RESID 1:10)
10	X-RAY DIFFRACTION	10	CHAIN H AND (RESID 11:15)
11	X-RAY DIFFRACTION	11	CHAIN H AND (RESID 16:30)
12	X-RAY DIFFRACTION	12	CHAIN H AND (RESID 31:45)
13	X-RAY DIFFRACTION	13	CHAIN H AND (RESID 46:54)
14	X-RAY DIFFRACTION	14	CHAIN E AND (RESID 19:33)
15	X-RAY DIFFRACTION	15	CHAIN E AND (RESID 34:61)
16	X-RAY DIFFRACTION	16	CHAIN E AND (RESID 62:81)

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