4K24 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   STRUCTURE OF ANTI-UPAR FAB ATN-658 IN COMPLEX WITH UPAR

Authors :   M. D. Huang, X. Xu, C. Yuan

Date :   08 Apr 13 (Deposition) - 26 Feb 14 (Release) - 05 Mar 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   4.50

Chains :   Asym. Unit : A,B,H,L,U
Biol. Unit 1: A,U  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: H,L  (1x)

Keywords :   Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   X. Xu, Y. Cai, Y. Wei, F. Donate, J. Juarez, G. Parry, L. Chen, E. J. Meehan, R. W. Ahn, A. Ugolkov, O. Dubrovskyi, T. V. O'Halloran, M. Huang, A. P. Mazar
Identification Of A New Epitope In Upar As A Target For The Cancer Therapeutic Monoclonal Antibody Atn-658, A Structura Homolog Of The Upar Binding Integrin Cd11B (Alpha M)
Plos One V. 9 85349 2014
PubMed-ID: 24465541 | Reference-DOI: 10.1371/JOURNAL.PONE.0085349

Molecule 1 - UROKINASE-TYPE PLASMINOGEN ACTIVATOR
	Chains	:	A
	EC Number	:	3.4.21.73
	Engineered	:	YES
	Expression System	:	DROSOPHILA MELANOGASTER
	Expression System Plasmid	:	PMT/BIP
	Expression System Strain	:	SCHNEIDER 2
	Expression System Taxid	:	7227
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 21-153
	Gene	:	PLAU
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	U-PLASMINOGEN ACTIVATOR, UPA, UROKINASE-TYPE PLASMINOGEN ACTIVATOR LONG CHAIN A, UROKINASE-TYPE PLASMINOGEN ACTIVATOR SHORT CHAIN A, UROKINASE-TYPE PLASMINOGEN ACTIVATOR CHAIN B

Molecule 2 - VITRONECTIN
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 21-60
	Gene	:	VTN
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	VN, S-PROTEIN, SERUM-SPREADING FACTOR, V75, VITRONECTIN V65 SUBUNIT, VITRONECTIN V10 SUBUNIT, SOMATOMEDIN-B

Molecule 3 - ANTI-UPAR ANTIBODY, HEAVY CHAIN
	Chains	:	H
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

Molecule 4 - ANTI-UPAR ANTIBODY, LIGHT CHAIN
	Chains	:	L
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

Molecule 5 - UROKINASE PLASMINOGEN ACTIVATOR SURFACE RECEPTOR
	Chains	:	U
	Engineered	:	YES
	Expression System	:	DROSOPHILA MELANOGASTER
	Expression System Plasmid	:	PMT/BIP
	Expression System Strain	:	SCHNEIDER 2
	Expression System Taxid	:	7227
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 23-303
	Gene	:	MO3, PLAUR, UPAR
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	U-PAR, UPAR, MONOCYTE ACTIVATION ANTIGEN MO3

		1	2	3	4	5
Asymmetric Unit	:	A	B	H	L	U
Biological Unit 1 (1x)	:	A				U
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			H	L

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 6)

No.	Name	Count	Type	Full Name
1	MAN	1	Ligand/Ion	ALPHA-D-MANNOSE
2	NAG	5	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 1 (2, 6)

No.	Name	Count	Type	Full Name
1	MAN	1	Ligand/Ion	ALPHA-D-MANNOSE
2	NAG	5	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	MAN	-1	Ligand/Ion	ALPHA-D-MANNOSE
2	NAG	-1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	MAN	-1	Ligand/Ion	ALPHA-D-MANNOSE
2	NAG	-1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN U:52 , VAL U:69 , NAG U:302	BINDING SITE FOR RESIDUE NAG U 301
2	AC2	SOFTWARE	SER U:81 , NAG U:301 , MAN U:303	BINDING SITE FOR RESIDUE NAG U 302
3	AC3	SOFTWARE	NAG U:302	BINDING SITE FOR RESIDUE MAN U 303
4	AC4	SOFTWARE	ASN U:172	BINDING SITE FOR RESIDUE NAG U 304
5	AC5	SOFTWARE	ASN U:200 , HIS U:203 , ASN U:233 , GLN U:234 , NAG U:306	BINDING SITE FOR RESIDUE NAG U 305
6	AC6	SOFTWARE	NAG U:305	BINDING SITE FOR RESIDUE NAG U 306

Asymmetric Unit

No.	Residues
1	A:11	-	A:19
2	A:13	-	A:31
3	A:33	-	A:42
4	A:50	-	A:131
5	A:71	-	A:113
6	A:102	-	A:126
7	B:5	-	B:21
8	B:5	-	B:32
9	B:9	-	B:39
10	B:19	-	B:32
11	B:25	-	B:31
12	H:22	-	H:92
13	H:140	-	H:195
14	L:23	-	L:88
15	L:134	-	L:194
16	U:3	-	U:24
17	U:3	-	U:17
18	U:6	-	U:12
19	U:17	-	U:45
20	U:71	-	U:76
21	U:95	-	U:122
22	U:98	-	U:105
23	U:115	-	U:147
24	U:153	-	U:170
25	U:171	-	U:176
26	U:194	-	U:222
27	U:197	-	U:205
28	U:215	-	U:241
29	U:247	-	U:265
30	U:266	-	U:271

Asymmetric Unit

No.	Residues
1	Ser H:95	-	Ile H:96
2	Ile H:96	-	Tyr H:97
3	Phe H:146	-	Pro H:147
4	Glu H:148	-	Pro H:149
5	Trp H:188	-	Pro H:189
6	Thr L:7	-	Pro L:8
7	Phe L:94	-	Pro L:95
8	Tyr L:140	-	Pro L:141

(no "SAP(SNP)/Variant" information available for 4K24)

(no "PROSITE Motif" information available for 4K24)

(no "Exon" information available for 4K24)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:125
                                                                                                                                                              
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeee.......eeee....ee.....ee......hhhhh...................hhhhhh........hhhhhh................eee........eee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                4k24 A    8 PSNCDCLNGGTCVSNKYFSNIHWCNCPKKFGGQHCEIDKSKTCYEGNGHFYRGKASTDTMGRPCLPWNSATVLQQTYHAHRSDALQLGLGKHNYCRNPDNRRRPWCYVQVGLKPLVQECMVHDCA  132
                                    17        27        37        47        57        67        77        87        97       107       117       127

Chain B from PDB  Type:PROTEIN  Length:40
                                                                         
               SCOP domains ---------------------------------------- SCOP domains
               CATH domains ---------------------------------------- CATH domains
               Pfam domains ---------------------------------------- Pfam domains
         Sec.struct. author ......................hhhhhh....hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------- PROSITE
                 Transcript ---------------------------------------- Transcript
                4k24 B    2 QESCKGRCTEGFNVDKKCQCDELCSYYQSCCTDYTAECKP   41
                                    11        21        31        41

Chain H from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                     
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....ee..eeee..hhhhh.eeeeeee...eeeeeeeee....ee..hhhhh..ee..ee....ee..ee...hhhhheeee..................eeee........eee......eee..eeeeee.....eeee.........eeeeeeee..eeeeeee.eee.........eeeeee....eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4k24 H    1 EVQLQQSGPELVKTGASVKISCKASGYSFTSYYMHWVKQSHGKSLEWIGEINPYNGGASYNQKIKGRATFTVDTSSRTAYMQFNSLTSEDSAVYYCARSIYGHSVLDYWGQGTSVSVSSAKTTPPSVYPLAPGSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSQTVTCNVAHPASSTKVDKKIVP  212
                                    10        20        30        40        50  |     59        69        79   |||  86        96    || 104       114       124  ||   140       150       160       170       180       190       200       210  
                                                                              52A                            82A||               100A|                        127|                                                                              
                                                                                                              82B|                100B                         134                                                                              
                                                                                                               82C

Chain L from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                           
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee.......eeee.............eeeee......eeeee.hhh........eeeeee..eeeeee........eeee.ee......ee...eeeeee.............hhhhhhhh.eeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeehhhhhh....eeeeee........ee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4k24 L    1 DVVMTQTPLTLSVTIGQPASISCKSSQSLLDSDGKTYLNWLLQRPGQSPKRLIYLVSKLDSGVPDRFTGSGSGTDFTLKISRVEAEDLGVYYCWQGTHFPLTFGAGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE  213
                                    10        20       27C||      35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205        
                                                     27A||||                                                                                                                                                                                          
                                                      27B|||                                                                                                                                                                                          
                                                       27C||                                                                                                                                                                                          
                                                        27D|                                                                                                                                                                                          
                                                         27E

Chain U from PDB  Type:PROTEIN  Length:273
                                                                                                                                                                                                                                                                                                                  
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.....eeee.......eeeeeeeeeee...eeeeeeeeee.........eee...eeee..eeee......................eeee...........ee........eee..eee...............eeeee........eeeee..eeeee....................eeeeeeeeeee...........eeeeee....eeeeeeeehhhhh...eeeeeehhhhhh..hhhhhh..eeeeeeee......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4k24 U    1 LRCMQCKTNGDCRVEECALGQDLCRTTIVRLWEEGEELELVEKSCTHSEKTNRTLSYRTGLKITSLTEVVCGLDLCNQGNSGVTYSRSRYLECISCGSSDMSCERGRHQSLQCRSPEEQCLDVVTHWIQEGEEGRPKDDRHLRGCGYLPGCPGSNGFHNNDTFHFLKCCNTTKCNEGPILELENLPQNGRQCYSCKGNSTHGCSSEETFLIDCRGPMNQCLVATGTHEPKNQSYMVRGCATASMCQHAHLGDAFSMNHIDVSCCTKSGCNHPD  275
                                    10        20        30        40        50        60        70        80 ||     92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272   
                                                                                                            82|                                                                                                                                                                                              
                                                                                                             85

Legend:		→ Mismatch	(orange background)
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		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

(no "SCOP Domain" information available for 4K24)

(no "CATH Domain" information available for 4K24)

(no "Pfam Domain" information available for 4K24)

Asymmetric Unit(hide GO term definitions)

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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Glu H:148 - Pro H:149	[ RasMol ]
		Ile H:96 - Tyr H:97	[ RasMol ]
		Phe H:146 - Pro H:147	[ RasMol ]
		Phe L:94 - Pro L:95	[ RasMol ]
		Ser H:95 - Ile H:96	[ RasMol ]
		Thr L:7 - Pro L:8	[ RasMol ]
		Trp H:188 - Pro H:189	[ RasMol ]
		Tyr L:140 - Pro L:141	[ RasMol ]

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	4k24
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 6)

Sites (6, 6)

SS Bonds (30, 30)

Cis Peptide Bonds (8, 8)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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