PDB-9pyf: uPA Inhibitory Fab AB2 Complex

ID or keywords:

Entry

Database: PDB / ID: 9pyf

Title

uPA Inhibitory Fab AB2 Complex

Components

AB2 Fab Heavy Chain
AB2 Fab Light Chain
Urokinase-type plasminogen activator

Keywords

PROTEIN BINDING / inhibitory antibody / serine protease / urokinase plasminogen activator / site directed

Function / homology

Function and homology information

u-plasminogen activator / regulation of smooth muscle cell-matrix adhesion / urokinase plasminogen activator signaling pathway / regulation of plasminogen activation / regulation of fibrinolysis / regulation of wound healing / protein complex involved in cell-matrix adhesion / regulation of signaling receptor activity / negative regulation of plasminogen activation / regulation of smooth muscle cell migration ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.9 Å

Authors

Anderson, K.J. / Bohn, M.F.

Funding support

1items

Citation

Journal: Biochim Biophys Acta Proteins Proteom / Year: 2021
Title: Structure of an affinity-matured inhibitory recombinant fab against urokinase plasminogen activator reveals basis of potency and specificity.
Authors: Sevillano, N. / Bohn, M.F. / Zimanyi, M. / Chen, Y. / Petzold, C. / Gupta, S. / Ralston, C.Y. / Craik, C.S.

History

Deposition	Aug 7, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 27, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9pyf.cif.gz	412.9 KB	Display	PDBx/mmCIF format
PDB format	pdb9pyf.ent.gz	335.2 KB	Display	PDB format
PDBx/mmJSON format	9pyf.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9pyf_validation.pdf.gz	467.2 KB	Display	wwPDB validaton report
Full document	9pyf_full_validation.pdf.gz	509.7 KB	Display
Data in XML	9pyf_validation.xml.gz	48.1 KB	Display
Data in CIF	9pyf_validation.cif.gz	63.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/py/9pyf ftp://data.pdbj.org/pub/pdb/validation_reports/py/9pyf	HTTPS FTP

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Related structure data

Similar structure data	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) #25 - Jan 2002 Thrombin similarity (8) #83 - Nov 2006 Fibrin similarity (8)

Deposited unit

A: AB2 Fab Light Chain

F: Urokinase-type plasminogen activator

I: AB2 Fab Light Chain

D: AB2 Fab Heavy Chain

H: AB2 Fab Heavy Chain

124 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: AB2 Fab Light Chain

D: AB2 Fab Heavy Chain

F: Urokinase-type plasminogen activator

defined by author
Evidence: homology
78.2 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

I: AB2 Fab Light Chain

H: AB2 Fab Heavy Chain

defined by author
46.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	86.745, 86.745, 172.420
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	78
Space group name H-M	P4₃

#1: Antibody	AB2 Fab Light Chain Mass: 23666.389 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Protein	Urokinase-type plasminogen activator / U-plasminogen activator / uPA Mass: 32114.633 Da / Num. of mol.: 1 / Mutation: C122A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PLAU / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P00749, u-plasminogen activator
#3: Antibody	AB2 Fab Heavy Chain Mass: 22459.205 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria)
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.61 Å³/Da / Density % sol: 52.84 %
Crystal grow	Temperature: 298.15 K / Method: vapor diffusion Details: For crystallization purposes, uPA was co-incubated with AB2 in a 1:1 stoichiometric ratio for 1h and co-purified using size-exclusion chromatography. The complex co-eluted was concentrated ...Details: For crystallization purposes, uPA was co-incubated with AB2 in a 1:1 stoichiometric ratio for 1h and co-purified using size-exclusion chromatography. The complex co-eluted was concentrated to 15 mg/mL.Crystallization drops were produced by mixing 0.1 uL of uPA-AB2 solution with 0.1 uL of the respective crystallization solution. A single crystal was produced using a solution containing 0.2 M diammonium hydrogen citrate (Salt) and 20 percent PEG 3350 and incubating the experiment for 14 days at room temperature.

Crystal

Density Matthews: 2.61 Å³/Da / Density % sol: 52.84 %

Crystal grow

Temperature: 298.15 K / Method: vapor diffusion
Details: For crystallization purposes, uPA was co-incubated with AB2 in a 1:1 stoichiometric ratio for 1h and co-purified using size-exclusion chromatography. The complex co-eluted was concentrated ...

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1158 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 1, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.1158 Å / Relative weight: 1
Reflection	Resolution: 2.9→86.745 Å / Num. obs: 28202 / % possible obs: 93.57 % / Redundancy: 73.1 % / B_iso Wilson estimate: 69.5 Å² / CC_1/2: 0.998 / CC star: 0.999 / Net I/σ(I): 10.81
Reflection shell	Resolution: 2.9→3.004 Å / Redundancy: 34.3 % / Num. unique obs: 2814 / CC_1/2: 0.833 / CC star: 0.953 / % possible all: 94.31

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Processing

Software

Name	Version	Classification
PHENIX	1.11.1_2575	refinement
xia2		data scaling
xia2		data reduction
PHENIX		phasing
PDB_EXTRACT		data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.9→86.745 Å / SU ML: 0.56 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 36.73 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2998	1270	4.81 %
R_work	0.2278	-	-
obs	0.2313	26386	93.56 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.9→86.745 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7600	0	0	44	7644

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	7767
X-RAY DIFFRACTION	f_angle_d	1.394	10472
X-RAY DIFFRACTION	f_dihedral_angle_d	18.573	4336
X-RAY DIFFRACTION	f_chiral_restr	0.067	1048
X-RAY DIFFRACTION	f_plane_restr	0.008	1417

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 (%)
2.9002-3.0163	0.4702	146	0.3962	2790	X-RAY DIFFRACTION	94
3.0163-3.1536	0.5045	121	0.3743	2653	X-RAY DIFFRACTION	89
3.1536-3.3199	0.3576	141	0.2982	2805	X-RAY DIFFRACTION	94
3.3199-3.5279	0.354	146	0.2706	2784	X-RAY DIFFRACTION	94
3.5279-3.8003	0.3412	134	0.2588	2765	X-RAY DIFFRACTION	93
3.8003-4.1827	0.3082	119	0.2386	2656	X-RAY DIFFRACTION	89
4.1827-4.7879	0.2385	147	0.1825	2796	X-RAY DIFFRACTION	94
4.7879-6.032	0.2745	166	0.1907	2864	X-RAY DIFFRACTION	96
6.032-86.745	0.2502	150	0.1824	3003	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	1.1316	-0.4345	0.8256	0.1315	0.161	2.9257	0.0941	0.2185	0.196	-0.1913	-0.2776	-0.1055	-0.0192	0.5612	0.0002	0.4507	0.065	0.0029	0.4809	0.0459	0.461	44.2853	77.6445	15.2259
2	0.7854	-0.9462	0.3309	0.2098	-0.2945	2.4622	-0.0411	0.2343	-0.2373	0.3633	0.0302	0.1349	0.0117	0.1837	0.0003	0.329	0.0427	0.0829	0.3261	0.0893	0.4068	24.4915	84.591	-15.6357
3	2.5761	0.6515	-0.0931	0.0891	-0.4913	1.4753	0.1121	0.4025	0.1739	-0.2206	-0.1504	0.1031	0.371	0.3622	0.0001	0.4123	0.0789	0.0282	0.5688	0.0423	0.4728	27.1725	85.8976	-17.9495
4	0.5098	-0.4388	0.3715	0.5602	-0.1751	0.1913	0.3934	-0.2482	-0.122	0.3024	-0.2249	-0.042	-0.1107	-0.0142	0.0129	0.7327	0.0679	0.0644	0.407	0.0263	0.5612	22.2168	54.9064	4.5198
5	2.9355	0.4494	0.4448	2.2313	0.9958	1.078	0.0906	-0.1036	-0.0877	0.3398	-0.02	-0.2951	0.001	0.1465	-0.0001	0.5831	-0.0023	-0.0104	0.3302	0.0332	0.3634	22.8694	45.2858	6.6541
6	1.6043	0.2103	-0.8409	2.6056	0.4648	3.3508	0.0182	-0.1586	-0.1299	0.2988	-0.2401	0.04	0.1027	0.0131	-0.0002	0.5706	0.021	0.0775	0.3399	0.0233	0.419	8.1237	46.5175	4.7804
7	0.6187	-0.1602	-0.3913	0.2932	-0.0906	0.2357	0.5954	0.1421	-0.2352	0.5198	-0.4734	0.0375	-0.2922	-0.3466	0.0041	1.6811	-0.0738	-0.272	1.0344	-0.0358	1.4829	61.5015	128.6289	3.4092
8	0.0597	-0.1628	-0.0615	0.3359	0.0079	0.631	2.3657	0.5934	1.5849	0.7345	-0.2445	0.4114	-1.519	0.7164	0.0712	1.5413	0.2324	0.0501	1.3448	0.2633	1.8228	47.9556	131.5789	-5.728
9	0.448	-0.2982	-0.2572	0.329	0.4753	0.624	0.7918	-1.177	-0.4869	-0.1181	-0.1959	-1.2414	-0.4308	0.6439	0.0014	1.12	-0.1443	-0.2882	0.9851	0.2587	1.5876	49.383	126.9751	8.1472
10	0.4163	-0.3327	0.2173	0.3067	0.0059	0.2749	1.8717	0.1625	-0.6073	0.8828	-0.2265	-0.0743	0.9838	-0.841	-0.0244	1.9712	-0.6483	0.0594	1.4797	0.1678	1.6076	56.2179	131.8355	9.9625
11	-0.0119	0.0395	0.0334	0.0256	0.1111	0.0641	0.2978	0.5722	-1.3176	-0.1331	-0.9145	-0.2928	0.0336	0.2922	-0.0018	1.2644	0.0016	-0.3601	0.9887	-0.0237	1.6075	51.83	121.4552	-1.3995
12	2.6432	-0.6965	-1.0037	0.1981	0.2012	0.2712	-0.0768	1.2083	0.8275	-0.0675	-0.4343	-0.8543	-0.1511	-0.0832	0.1796	1.153	-0.5556	-0.4139	0.372	-0.0886	1.9523	70.9148	118.458	20.2374
13	-0.0047	0.006	0.1884	0.064	0.0433	0.8755	0.452	-0.2563	0.8541	0.4214	-0.2536	-1.5684	2.2797	1.2115	0.0702	2.0335	-0.4193	-0.0309	1.4308	0.5101	1.8942	77.0555	103.8474	23.5028
14	0.1734	-0.1178	-0.2443	0.258	0.4574	0.5141	0.9638	-1.0821	-0.575	-0.2306	0.1798	0.2072	-0.3431	1.3303	0.0017	0.8945	-0.013	-0.0711	1.4725	-0.2457	1.7365	75.6928	108.0654	19.1594
15	1.1839	0.4471	2.2758	1.1783	0.623	4.5515	1.8281	-0.1733	0.457	-0.2808	1.079	-0.5848	0.4213	1.4865	0.7406	1.0728	-0.0931	0.7647	1.4844	-0.211	3.2723	84.8298	103.2372	25.6571
16	0.1565	0.1444	-0.4322	0.8495	0.2059	1.8144	-0.689	-0.1338	-0.0906	0.8638	-0.1081	0.159	0.8278	0.3419	-0.0332	0.9227	-0.745	0.5655	1.3977	-0.045	1.7668	82.6142	106.2679	32.6593
17	2.5283	-0.8678	1.1919	1.9661	-1.5781	1.2609	0.0543	-0.1829	0.0514	0.1887	-0.1696	0.0596	-0.302	-0.3785	-0	0.42	0.1138	-0.0322	0.5715	-0.1625	0.4388	24.3432	86.2715	22.658
18	-0.0334	-0.0777	-0.0551	0.3111	-0.4362	0.6867	0.3417	0.1145	0.3282	0.0315	0.0613	-0.2099	0.4232	0.3318	-0.0007	0.5944	0.006	0.0285	0.5651	-0.0297	0.4879	17.6692	75.8608	-16.003
19	1.6028	-0.3645	0.0517	2.6189	-1.0054	1.5977	-0.2367	-0.1023	0.0818	0.4387	0.2498	0.174	0.2793	-0.2143	0.0003	0.3465	0.0673	0.0514	0.2884	-0.0048	0.3341	17.4111	79.5145	-4.3895
20	0.6876	0.3601	-0.128	0.4511	-0.69	0.8212	0.8097	-0.14	-0.6347	-0.6764	-0.6749	-0.1269	-0.3492	0.2681	-0.0001	1.2822	-0.0598	-0.3775	0.9476	0.2655	1.5409	41.6804	105.0669	6.0975
21	0.2366	0.0008	-0.3987	0.0032	-0.0204	0.6415	-1.4531	-0.1654	0.1908	-0.5517	0.03	-0.3802	1.6403	0.4474	-0.1369	1.5601	-0.0563	-1.0065	1.2826	0.4349	2.2955	53.0571	111.4004	0.2918
22	0.1425	-0.0879	-0.0882	0.0975	0.0166	0.0673	0.2657	-0.1108	-1.0324	0.1222	-0.8885	0.3598	-0.8353	-2.5267	0.0031	1.5397	0.3102	-0.5753	1.5027	-0.4488	1.4386	33.8196	113.22	-4.1136
23	0.0218	-0.0281	0.0267	0.0047	-0.0261	0.0219	-0.076	-0.3015	-1.0337	-0.2367	1.1518	-0.5411	0.2825	0.055	-0.0018	1.1476	-0.1768	-0.0583	0.8989	-0.0487	2.0439	46.0044	107.481	-9.5754
24	2.7727	-0.8891	-1.0591	0.3345	0.6979	1.2257	0.0677	0.1914	-3.0838	1.7605	0.1038	-0.6443	1.4055	0.8352	-0.1582	1.0211	0.1954	-0.5162	0.8557	0.1264	1.8806	43.3386	102.829	0.0254
25	1.4523	-0.6107	-0.0613	0.3755	0.2243	0.3454	-0.6383	-1.1662	-1.0382	-0.3455	1.1486	-0.4103	1.657	-0.0483	0.1264	1.72	-0.1194	-0.5732	0.7962	0.3146	1.7334	46.4523	111.8927	6.9719
26	0.2116	0.2588	0.1668	0.0221	0.0702	1.6541	0.6728	-0.1301	0.5517	0.3338	1.8562	0.147	0.6976	-0.7902	0.1746	1.8691	-0.0096	-0.682	0.8999	0.1055	2.3149	65.6766	96.6294	19.8538
27	0.446	-0.1201	-0.1776	0.1121	-0.0421	0.125	-0.597	-0.5825	-0.0701	1.7533	-0.6199	0.6735	-1.2924	-0.2864	-0.0008	2.2297	-0.1237	-0.4723	1.3249	-0.1731	1.2653	66.7808	102.7256	25.8618
28	0.1088	-0.0538	0.0708	0.0139	-0.0247	0.059	-1.1036	-2.1821	0.3771	2.3025	-0.2588	0.5437	-0.5155	-0.748	-0.0053	2.1848	-0.1922	-0.0733	1.7308	-0.1572	1.2661	59.633	106.7402	25.091
29	0.298	0.302	-0.0169	0.3296	-0.042	0.0417	0.7211	-0.2974	0.1461	-0.2585	-0.4108	-0.3882	0.8264	0.2025	-0.0193	1.6151	0.0875	-0.0853	1.0821	-0.6553	3.976	69.2988	97.1626	11.6175
30	1.044	-0.0216	0.4293	0.0111	0.0702	0.3846	0.8247	-3.7823	0.6149	2.5447	-0.6057	-0.1967	-0.764	-0.4453	0.0008	3.408	-0.5912	0.2414	1.8872	-0.5563	1.3526	64.1378	106.1266	35.1908
31	4.1699	-1.9745	-2.3112	4.0159	-0.657	2.3344	0.373	2.0476	0.4197	-1.9297	-0.2138	0.0578	0.0298	-0.6897	0.1362	1.1969	-1.4017	-0.0751	0.4303	0.0112	1.1876	58.5913	95.842	24.7806

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 118 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 119 through 155 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 156 through 218 )
4	X-RAY DIFFRACTION	4	chain 'F' and (resid 16 through 37D)
5	X-RAY DIFFRACTION	5	chain 'F' and (resid 38 through 140 )
6	X-RAY DIFFRACTION	6	chain 'F' and (resid 141 through 244 )
7	X-RAY DIFFRACTION	7	chain 'I' and (resid 1 through 18 )
8	X-RAY DIFFRACTION	8	chain 'I' and (resid 19 through 37 )
9	X-RAY DIFFRACTION	9	chain 'I' and (resid 38 through 73 )
10	X-RAY DIFFRACTION	10	chain 'I' and (resid 74 through 88 )
11	X-RAY DIFFRACTION	11	chain 'I' and (resid 89 through 106 )
12	X-RAY DIFFRACTION	12	chain 'I' and (resid 107 through 125 )
13	X-RAY DIFFRACTION	13	chain 'I' and (resid 126 through 155 )
14	X-RAY DIFFRACTION	14	chain 'I' and (resid 156 through 187 )
15	X-RAY DIFFRACTION	15	chain 'I' and (resid 188 through 206 )
16	X-RAY DIFFRACTION	16	chain 'I' and (resid 207 through 218 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 2 through 121 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 122 through 136 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 137 through 215 )
20	X-RAY DIFFRACTION	20	chain 'H' and (resid 2 through 34 )
21	X-RAY DIFFRACTION	21	chain 'H' and (resid 35 through 47 )
22	X-RAY DIFFRACTION	22	chain 'H' and (resid 48 through 58 )
23	X-RAY DIFFRACTION	23	chain 'H' and (resid 59 through 69 )
24	X-RAY DIFFRACTION	24	chain 'H' and (resid 70 through 94 )
25	X-RAY DIFFRACTION	25	chain 'H' and (resid 95 through 112 )
26	X-RAY DIFFRACTION	26	chain 'H' and (resid 113 through 133 )
27	X-RAY DIFFRACTION	27	chain 'H' and (resid 134 through 150 )
28	X-RAY DIFFRACTION	28	chain 'H' and (resid 151 through 170 )
29	X-RAY DIFFRACTION	29	chain 'H' and (resid 171 through 180 )
30	X-RAY DIFFRACTION	30	chain 'H' and (resid 181 through 198 )
31	X-RAY DIFFRACTION	31	chain 'H' and (resid 199 through 215 )

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About Yorodumi

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Yorodumi