PDB-5nmv: Crystal structure of 2F22 Fab fragment against TFPI1

ID or keywords:

Entry

Database: PDB / ID: 5nmv

Title

Crystal structure of 2F22 Fab fragment against TFPI1

Components

Fab heavy chain
Fab light chain
Tissue factor pathway inhibitor

Keywords

IMMUNE SYSTEM / Fab

Function / homology

Function and homology information

negative regulation of blood coagulation / Extrinsic Pathway of Fibrin Clot Formation / cellular response to steroid hormone stimulus / endopeptidase inhibitor activity / side of membrane / serine-type endopeptidase inhibitor activity / caveola / blood coagulation / cell surface / endoplasmic reticulum ...
Similarity search - Function

Biological species

Mus (mice)

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.65 Å

Authors

Svensson, L.A. / Petersen, H.H.

Citation

Journal: J. Thromb. Haemost. / Year: 2018
Title: Factor Xa and VIIa inhibition by tissue factor pathway inhibitor is prevented by a monoclonal antibody to its Kunitz-1 domain.
Authors: Augustsson, C. / Svensson, A. / Kjaer, B. / Chao, T.Y. / Wenjuan, X. / Krogh, B.O. / Breinholt, J. / Clausen, J.T. / Hilden, I. / Petersen, H.H. / Petersen, L.C.

History

Deposition	Apr 7, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 28, 2018	Provider: repository / Type: Initial release
Revision 1.1	May 9, 2018	Group: Data collection / Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2	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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PDBx/mmCIF format	5nmv.cif.gz	302.7 KB	Display	PDBx/mmCIF format
PDB format	pdb5nmv.ent.gz	250.8 KB	Display	PDB format
PDBx/mmJSON format	5nmv.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5nmv_validation.pdf.gz	447.6 KB	Display	wwPDB validaton report
Full document	5nmv_full_validation.pdf.gz	449 KB	Display
Data in XML	5nmv_validation.xml.gz	25.4 KB	Display
Data in CIF	5nmv_validation.cif.gz	37.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nm/5nmv ftp://data.pdbj.org/pub/pdb/validation_reports/nm/5nmv	HTTPS FTP

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Related structure data

Similar structure data	6z7w-6 5e8d-d 5kn5-1 6z7w-5 5u3j-d 6z7w-3 6z7w-1 3nh7-2 3pnw-3 3pnw-4 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	#21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1) #79 - Jul 2006 Amyloid-beta Precursor Protein similarity (7) #189 - Sep 2015 Amyloids similarity (7) #46 - Oct 2003 Trypsin similarity (7) #75 - Mar 2006 Tissue Factor similarity (1) #142 - Oct 2011 PDB Pioneers similarity (7)

Deposited unit

L: Fab light chain

H: Fab heavy chain

K: Tissue factor pathway inhibitor

hetero molecules

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

1

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	89.010, 66.660, 106.110
Angle α, β, γ (deg.)	90.00, 111.18, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Antibody	Fab light chain Mass: 23242.828 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus (mice) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Antibody	Fab heavy chain Mass: 23814.689 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus (mice) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#3: Protein	Tissue factor pathway inhibitor / TFPI / Extrinsic pathway inhibitor / EPI / Lipoprotein-associated coagulation inhibitor / LACI Mass: 9797.940 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TFPI, LACI, TFPI1 Cell line (production host): HUMAN EMBRYONIC KIDNEY 293 CELLS Production host: Homo sapiens (human) / References: UniProt: P10646
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 489 / 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: 2.58 Å³/Da / Density % sol: 52.35 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20 % PEG 3350 200 mM Potassium formate

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å
Detector	Type: MARRESEARCH / Detector: CCD / Date: Mar 26, 2008
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.65→27.642 Å / Num. obs: 301437 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / CC_1/2: 0.998 / R_merge(I) obs: 0.084 / R_rim(I) all: 0.096 / Net I/σ(I): 9.56
Reflection shell	Resolution: 1.65→1.69 Å / Redundancy: 3.8 % / R_merge(I) obs: 2.28 / Mean I/σ(I) obs: 0.67 / Num. unique obs: 19462 / CC_1/2: 0.16 / R_rim(I) all: 2.67 / % possible all: 99.2

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Processing

Software

Name	Version	Classification
PHENIX	(dev_2283: ???)	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.65→27.642 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 25.33

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2022	3379	4.87 %	Random selection
R_work	0.1752	-	-	-
obs	0.1766	69448	99.61 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 1.65→27.642 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3802	0	24	489	4315

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	4024
X-RAY DIFFRACTION	f_angle_d	1.07	5481
X-RAY DIFFRACTION	f_dihedral_angle_d	12.744	2444
X-RAY DIFFRACTION	f_chiral_restr	0.06	603
X-RAY DIFFRACTION	f_plane_restr	0.007	705

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 (%)
1.6499-1.6735	0.439	154	0.4068	2703	X-RAY DIFFRACTION	99
1.6735-1.6985	0.3711	130	0.3914	2743	X-RAY DIFFRACTION	99
1.6985-1.725	0.3577	120	0.3464	2746	X-RAY DIFFRACTION	99
1.725-1.7533	0.3298	125	0.3338	2753	X-RAY DIFFRACTION	99
1.7533-1.7835	0.342	144	0.3061	2760	X-RAY DIFFRACTION	100
1.7835-1.8159	0.2778	126	0.2782	2728	X-RAY DIFFRACTION	100
1.8159-1.8509	0.2951	134	0.2493	2821	X-RAY DIFFRACTION	100
1.8509-1.8886	0.2659	123	0.2358	2695	X-RAY DIFFRACTION	100
1.8886-1.9297	0.254	141	0.2286	2747	X-RAY DIFFRACTION	100
1.9297-1.9746	0.2432	141	0.213	2750	X-RAY DIFFRACTION	100
1.9746-2.0239	0.2258	126	0.2006	2786	X-RAY DIFFRACTION	100
2.0239-2.0786	0.2093	139	0.1846	2726	X-RAY DIFFRACTION	100
2.0786-2.1398	0.2154	149	0.1804	2758	X-RAY DIFFRACTION	100
2.1398-2.2088	0.2052	142	0.1681	2726	X-RAY DIFFRACTION	100
2.2088-2.2877	0.2016	147	0.171	2754	X-RAY DIFFRACTION	100
2.2877-2.3793	0.208	149	0.1729	2733	X-RAY DIFFRACTION	100
2.3793-2.4875	0.2089	155	0.1703	2751	X-RAY DIFFRACTION	100
2.4875-2.6185	0.2025	140	0.1642	2759	X-RAY DIFFRACTION	100
2.6185-2.7825	0.2235	152	0.1614	2774	X-RAY DIFFRACTION	100
2.7825-2.997	0.1913	126	0.1662	2740	X-RAY DIFFRACTION	100
2.997-3.2982	0.2224	162	0.1541	2765	X-RAY DIFFRACTION	100
3.2982-3.7744	0.1766	146	0.1472	2760	X-RAY DIFFRACTION	99
3.7744-4.7515	0.1308	175	0.1199	2753	X-RAY DIFFRACTION	100
4.7515-27.6455	0.1543	133	0.1432	2838	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	7.1145	-6.6495	0.38	7.6517	-1.0908	2.1825	0.4087	0.3745	0.695	-0.3846	-0.2921	-0.5253	-0.2975	0.5177	-0.0225	0.3486	-0.1044	0.0534	0.4235	-0.0152	0.3383	24.8435	70.5972	34.018
2	3.462	-0.4629	0.2986	0.8741	-0.0397	2.0274	0.1282	-0.0867	0.1231	-0.0105	0.0254	-0.0905	-0.156	0.2746	-0.1465	0.225	-0.0199	0.0192	0.209	-0.037	0.1642	17.188	67.5315	39.2081
3	2.4531	0.0637	1.7239	1.6497	1.289	8.0219	0.1032	-0.1439	0.0929	-0.1208	-0.1206	-0.0743	0.0304	0.1437	0.0134	0.1316	0.0457	0.0218	0.2157	0.0145	0.1766	30.8073	60.1338	7.2679
4	2.3324	0.2398	-1.8422	3.6122	-2.1151	9.0205	0.065	0.0513	0.2725	-0.12	-0.0228	-0.182	-0.3549	0.3067	-0.0217	0.2498	0.021	0.0101	0.1756	0.0051	0.2471	27.3478	68.2665	1.6733
5	2.6122	0.6038	0.3325	1.7511	-0.0486	5.7604	-0.1424	0.0022	0.0657	-0.3213	-0.0025	-0.1879	-0.1127	0.4958	0.095	0.2273	0.0666	0.0289	0.18	-0.0019	0.2168	32.1625	61.4218	4.1479
6	1.9029	-0.3346	0.0236	2.3003	-1.3918	7.5625	0.2586	0.1394	-0.1081	-0.1352	-0.194	0.2349	0.4626	-0.1814	-0.0987	0.2109	0.0085	-0.0267	0.1617	-0.0159	0.2254	-3.0218	57.7233	28.7227
7	4.5248	-1.3732	0.8431	3.0758	1.3855	1.2244	0.2589	0.2727	0.2676	-0.2017	-0.2098	-0.001	-0.2638	-0.1588	-0.0422	0.268	0.0457	-0.0049	0.1715	0.0116	0.1791	-0.5065	69.3483	30.8693
8	0.9852	-0.3793	-1.096	0.5497	0.48	1.7117	0.0082	0.0714	-0.1225	-0.0074	-0.108	0.0612	-0.0038	-0.0607	0.0831	0.2121	0.0517	-0.0198	0.179	0.0067	0.1895	11.9888	56.9288	17.4036
9	5.9001	-4.0469	-0.0047	4.9037	0.3	3.2299	0.0894	0.2466	-0.3629	-0.013	-0.2483	0.3433	0.3484	0.0323	0.1931	0.2668	0.0419	0.0185	0.1803	-0.0166	0.2318	20.0254	42.5822	6.5172
10	4.6961	-0.1818	0.5211	4.9247	4.8421	4.8896	0.3817	-0.6329	-0.6709	1.4283	-0.6026	0.2197	0.8261	-0.1744	0.3714	0.3988	0.0021	0.0167	0.3727	0.0576	0.3018	3.9912	61.4643	50.7841
11	6.0194	-1.3172	1.1703	4.9191	1.9574	5.5838	0.0359	-0.1714	-0.1861	-0.1409	-0.1363	0.1411	-0.2489	-0.4607	0.1064	0.2666	0.0526	0.0313	0.235	-0.0474	0.2435	-7.1066	79.993	43.9269
12	3.2147	0.0706	0.59	7.9323	4.8199	3.1909	-0.0738	-0.2643	-0.1781	0.281	-0.5418	0.6254	0.2592	-0.6227	0.5873	0.254	0.0594	0.0535	0.3707	-0.0368	0.3127	-10.5086	81.9244	50.7774
13	5.4549	0.1162	1.3534	5.719	2.538	1.5355	0.1728	-0.0751	0.1607	-0.3077	-0.3191	0.2809	-0.3311	-0.2602	0.126	0.2629	0.0592	0.0103	0.2397	-0.0351	0.2163	-5.2151	76.8749	41.7009
14	1.9802	-2.7219	1.0827	7.4453	3.616	7.8529	-0.1707	-0.7311	-0.4214	0.5832	-0.2282	0.4239	0.6562	-0.5548	0.3748	0.3854	0.0005	0.0929	0.3989	-0.0063	0.2715	-8.0249	71.4981	54.0247

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'L' and (resid 1 through 18 )
2	X-RAY DIFFRACTION	2	chain 'L' and (resid 19 through 105 )
3	X-RAY DIFFRACTION	3	chain 'L' and (resid 106 through 149 )
4	X-RAY DIFFRACTION	4	chain 'L' and (resid 150 through 162 )
5	X-RAY DIFFRACTION	5	chain 'L' and (resid 163 through 212 )
6	X-RAY DIFFRACTION	6	chain 'H' and (resid 1 through 33 )
7	X-RAY DIFFRACTION	7	chain 'H' and (resid 34 through 63 )
8	X-RAY DIFFRACTION	8	chain 'H' and (resid 64 through 196 )
9	X-RAY DIFFRACTION	9	chain 'H' and (resid 197 through 221 )
10	X-RAY DIFFRACTION	10	chain 'K' and (resid 15 through 22 )
11	X-RAY DIFFRACTION	11	chain 'K' and (resid 23 through 45 )
12	X-RAY DIFFRACTION	12	chain 'K' and (resid 46 through 56 )
13	X-RAY DIFFRACTION	13	chain 'K' and (resid 57 through 68 )
14	X-RAY DIFFRACTION	14	chain 'K' and (resid 69 through 77 )

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