4K24: Anti-uPAR Fab ATN-658

Structure of anti-uPAR Fab ATN-658 in complex with uPAR. Determined by X-ray diffraction at 4.5 Å resolution. Released 26 Feb 2014.

Method: X-ray diffraction
Resolution: 4.5 Å
Organisms: Homo sapiens, Mus musculus
Chains: 5
Atoms: 6,771
Mol. weight: 101.42 kDa
Ligands: NAG, MAN
Released: 26 Feb 2014

Explore 4K24 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4K24 contains 21 α-helices and 85 β-strands across 5 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 4 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	18-21	4	1
β-strand	29-32	4	1
β-strand	37-38	2	2
β-strand	44-45	2	2
β-strand	51	1	3
α-helix	53-55	3
α-helix	77-80	4
α-helix	91-94	4
β-strand	103	1	4
β-strand	112-114	3	4
β-strand	123-125	3	4
α-helix	126-127	2
β-strand	130	1	3

Chain B: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	25-28	4
α-helix	35-38	4

Chain H: 5 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	5
β-strand	10-12	3	6
β-strand	18-19	2	7
β-strand	22-25	4	5
α-helix	29-31	3
β-strand	34-40	7	6
β-strand	44-52	9	6
β-strand	56-57	2	6
α-helix	61-63	3
β-strand	67-68	2	7
β-strand	71-72	2	5
β-strand	77-78	2	5
β-strand	81-82	2	7
α-helix	84-86	3
β-strand	88-91	4	6
β-strand	93	1	8
β-strand	94	1	6
β-strand	103	1	8
β-strand	108-111	4	6
α-helix	115-116	2
β-strand	117	1	9
β-strand	120-122	3	10
β-strand	135-137	3	11
β-strand	140-145	6	10
β-strand	146	1	9
β-strand	151-154	4	12
β-strand	159	1	12
β-strand	164-171	8	10
β-strand	174-180	7	10
β-strand	182-184	3	11
β-strand	194-199	6	12
α-helix	200-202	3
β-strand	204-209	6	12

Chain L: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	13
β-strand	10-14	5	14
β-strand	19	1	13
β-strand	22-25	4	13
β-strand	27D	1	15
β-strand	30	1	15
β-strand	34-38	5	14
β-strand	45-49	5	14
α-helix	50-52	3
β-strand	54	1	14
β-strand	62-67	6	13
β-strand	70-75	6	13
β-strand	84-87	4	14
β-strand	89-90	2	16
α-helix	96	1
β-strand	97-98	2	16
β-strand	102-107	6	14
β-strand	117	1	17
α-helix	119-121	3
α-helix	122-127	6
β-strand	130-139	10	17
β-strand	145-150	6	18
β-strand	153-155	3	18
β-strand	159-163	5	17
α-helix	165-167	3
β-strand	173-181	9	17
α-helix	183-186	4
β-strand	192-197	6	18
α-helix	204-205	2
β-strand	206-207	2	18

Chain U: 3 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	19
β-strand	12-15	4	19
β-strand	23-33	11	19
β-strand	37-46	10	19
β-strand	53	1	19
β-strand	56-58	3	19
β-strand	62-65	4	19
β-strand	68-71	4	19
β-strand	96-97	2	20
β-strand	98-99	2	21
β-strand	111-112	2	20
β-strand	121-123	3	19
β-strand	126-128	3	22
β-strand	143	1	22
β-strand	144-145	2	21
β-strand	146-148	3	19
β-strand	157-161	5	22
β-strand	164-168	5	22
β-strand	171	1	19
β-strand	189-196	8	23
β-strand	197-199	3	22
β-strand	211-216	6	23
β-strand	221-228	8	22
α-helix	230-232	3
β-strand	237-242	6	22
α-helix	244-247	4
α-helix	252-255	4
β-strand	259-266	8	22

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Urokinase-type plasminogen activator	A	protein	135	Homo sapiens	P00749 (AlphaFold model)
Vitronectin	B	protein	40	Homo sapiens	P04004 (AlphaFold model)
anti-uPAR antibody, heavy chain	H	protein	228	Mus musculus
anti-uPAR antibody, light chain	L	protein	219	Mus musculus
Urokinase plasminogen activator surface receptor	U	protein	283	Homo sapiens	Q03405 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4K24_1 Urokinase-type plasminogen activator (chains A)
RSSNELHQVPSNCDCLNGGTCVSNKYFSNIHWCNCPKKFGGQHCEIDKSKTCYEGNGHFY
RGKASTDTMGRPCLPWNSATVLQQTYHAHRSDALQLGLGKHNYCRNPDNRRRPWCYVQVG
LKPLVQECMVHDCAD

Sequence of entity 2 (B), FASTA

>4K24_2 Vitronectin (chains B)
QESCKGRCTEGFNVDKKCQCDELCSYYQSCCTDYTAECKP

Sequence of entity 3 (H), FASTA

>4K24_3 anti-uPAR antibody, heavy chain (chains H)
EVQLQQSGPELVKTGASVKISCKASGYSFTSYYMHWVKQSHGKSLEWIGEINPYNGGASY
NQKIKGRATFTVDTSSRTAYMQFNSLTSEDSAVYYCARSIYGHSVLDYWGQGTSVSVSSA
KTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDL
YTLSSSVTVPSSTWPSQTVTCNVAHPASSTKVDKKIVPRDCGCKPCIC

Sequence of entity 4 (L), FASTA

>4K24_4 anti-uPAR antibody, light chain (chains L)
DVVMTQTPLTLSVTIGQPASISCKSSQSLLDSDGKTYLNWLLQRPGQSPKRLIYLVSKLD
SGVPDRFTGSGSGTDFTLKISRVEAEDLGVYYCWQGTHFPLTFGAGTKLELKRADAAPTV
SIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSM
SSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 5 (U), FASTA

>4K24_5 Urokinase plasminogen activator surface receptor (chains U)
RSLRCMQCKTNGDCRVEECALGQDLCRTTIVRLWEEGEELELVEKSCTHSEKTNRTLSYR
TGLKITSLTEVVCGLDLCNQGNSGRAVTYSRSRYLECISCGSSDMSCERGRHQSLQCRSP
EEQCLDVVTHWIQEGEEGRPKDDRHLRGCGYLPGCPGSNGFHNNDTFHFLKCCNTTKCNE
GPILELENLPQNGRQCYSCKGNSTHGCSSEETFLIDCRGPMNQCLVATGTHEPKNQSYMV
RGCATASMCQHAHLGDAFSMNHIDVSCCTKSGCNHPDLDVQYR

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1
MAN	alpha-D-mannopyranose	C6 H12 O6	1

Primary citation

Identification of a New Epitope in uPAR as a Target for the Cancer Therapeutic Monoclonal Antibody ATN-658, a Structural Homolog of the uPAR Binding Integrin CD11b ( alpha M). Xu, X., Cai, Y., Wei, Y. et al. PLoS One (2014) 9:e85349-e85349. DOI 10.1371/journal.pone.0085349 · PubMed

Other PDB entries of the same protein (UniProt P00749 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5YC6 1.18 Å, The crystal structure of uPA in complex with 4-Bromobenzylamirne at pH4.6
4ZKO 1.29 Å, The crystal structure of upain-1-W3A in complex with uPA at pH7.4
4ZKN 1.36 Å, The crystal structure of upain-1-W3A in complex with uPA at pH5.5
4ZKR 1.36 Å, The crystal structure of upain-1-W3A in complex with uPA at pH9.0
6XVD 1.4 Å, Crystal structure of complex of urokinase and a upain-1 variant(W3F) in pH7.4 condition
2O8T 1.45 Å, Crystal Structure and Binding Epitopes of Urokinase-type Plasminogen Activator…
3MHW 1.45 Å, The complex crystal Structure of Urokianse and 2-Aminobenzothiazole
5Z1C 1.45 Å, The crystal structure of uPA in complex with 4-Iodobenzylamine at pH7.4
5WXF 1.46 Å, Crystal structure of uPA in complex with upain-2-2
4MNW 1.49 Å, Crystal structure of urokinase-type plasminogen activator (uPA) complexed with bicyclic…
1GJ7 1.5 Å, Engineering inhibitors highly selective for the S1 sites of SER190 trypsin-like serine…
4XSK 1.5 Å, Structure of PAItrap, an uPA mutant

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