4K2U - JenaLib

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Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF PFEBA-175 F1 IN COMPLEX WITH R218 ANTIBODY FAB FRAGMENT

Authors :   N. H. Tolia

Date :   09 Apr 13 (Deposition) - 12 Jun 13 (Release) - 12 Jun 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.45

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

Keywords :   Dbl Domain, Immunoglobulin Domain, Antibody Fragment, Cell Attachment, Immunity, Receptor, Ligand, Extracellular, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Chen, M. M. Paing, N. Salinas, B. K. Sim, N. H. Tolia
Structural And Functional Basis For Inhibition Of Erythrocyte Invasion By Antibodies That Target Plasmodium Falciparum Eba-175.
Plos Pathog. V. 9 03390 2013
PubMed-ID: 23717209 | Reference-DOI: 10.1371/JOURNAL.PPAT.1003390

Molecule 1 - ERYTHROCYTE BINDING ANTIGEN 175
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	EBA-175, MAL7P1.176
	Organism Scientific	:	PLASMODIUM FALCIPARUM
	Organism Taxid	:	36329

Molecule 2 - ANTIBODY HEAVY CHAIN
	Chains	:	H, I
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

Molecule 3 - ANTIBODY LIGHT CHAIN
	Chains	:	L, M
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	H	I	L	M
Biological Unit 1 (1x)	:	A		H		L
Biological Unit 2 (1x)	:		B		I		M

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 12)

No.	Name	Count	Type	Full Name
1	SO4	12	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 7)

No.	Name	Count	Type	Full Name
1	SO4	7	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 5)

No.	Name	Count	Type	Full Name
1	SO4	5	Ligand/Ion	SULFATE ION

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASN A:168 , HOH A:422	BINDING SITE FOR RESIDUE SO4 A 301
02	AC2	SOFTWARE	LYS A:230	BINDING SITE FOR RESIDUE SO4 A 302
03	AC3	SOFTWARE	LYS B:61 , LYS B:150	BINDING SITE FOR RESIDUE SO4 B 301
04	AC4	SOFTWARE	ARG H:94 , ASP H:97 , HOH H:402 , HOH H:417	BINDING SITE FOR RESIDUE SO4 H 301
05	AC5	SOFTWARE	HIS H:164 , ASP L:167	BINDING SITE FOR RESIDUE SO4 H 302
06	AC6	SOFTWARE	ASN A:164 , TYR H:33 , TRP H:47 , ARG H:50 , LYS H:58 , TYR H:100B , HOH H:413 , PHE L:94 , TRP L:96	BINDING SITE FOR RESIDUE SO4 H 303
07	AC7	SOFTWARE	VAL I:183 , THR I:187 , TRP I:188 , GLU I:191 , THR I:192 , VAL I:193 , HOH I:420	BINDING SITE FOR RESIDUE SO4 I 301
08	AC8	SOFTWARE	PHE I:27 , ARG I:94 , ASP I:97 , HOH I:434	BINDING SITE FOR RESIDUE SO4 I 302
09	AC9	SOFTWARE	ASN B:164 , TYR I:33 , TRP I:47 , ARG I:50 , LYS I:58 , TYR I:100B , HOH I:418 , PHE M:94 , TRP M:96	BINDING SITE FOR RESIDUE SO4 I 303
10	BC1	SOFTWARE	GLU H:101 , TYR L:49 , LEU L:54 , HIS L:55 , SER L:56 , HOH L:402	BINDING SITE FOR RESIDUE SO4 L 301
11	BC2	SOFTWARE	TYR L:210	BINDING SITE FOR RESIDUE SO4 L 302
12	BC3	SOFTWARE	TYR M:49 , HIS M:55 , SER M:56	BINDING SITE FOR RESIDUE SO4 M 301

Asymmetric Unit

No.	Residues
1	A:14	-	A:45
2	A:25	-	A:36
3	A:88	-	A:166
4	A:219	-	A:281
5	B:14	-	B:45
6	B:25	-	B:36
7	B:202	-	B:215
8	B:211	-	B:283
9	B:219	-	B:281
10	H:22	-	H:92
11	H:140	-	H:195
12	I:22	-	I:92
13	I:140	-	I:195
14	L:23	-	L:88
15	L:134	-	L:194
16	M:23	-	M:88
17	M:134	-	M:194

Asymmetric Unit

No.	Residues
1	Phe H:146	-	Pro H:147
2	Glu H:148	-	Pro H:149
3	Trp H:188	-	Pro H:189
4	Phe I:146	-	Pro I:147
5	Glu I:148	-	Pro I:149
6	Trp I:188	-	Pro I:189
7	Phe L:94	-	Pro L:95
8	Tyr L:140	-	Pro L:141
9	Lys L:199	-	Lys L:200
10	Arg L:209	-	Tyr L:210
11	Thr M:7	-	Thr M:8
12	Phe M:94	-	Pro M:95
13	Tyr M:140	-	Pro M:141

(no "SAP(SNP)/Variant" information available for 4K2U)

(no "PROSITE Motif" information available for 4K2U)

(no "Exon" information available for 4K2U)

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:230
                                                                                                                                                                                                                                                                       
               SCOP domains d4k2ua_ A: automated matches                                                                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeee......eeeehhhhh..hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh....hhhhh......hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4k2u A   10 VLSNCREKRKGMKWDCKKKNDNYVCIPDRRIQLCIVNLSIIKTYTKETMKDHFIEASKKESQLLLKKNDNKYNSKFCNDLKNSFLDYGHLAMGNDMDFGGYSTKAENKIQEVFKGAHHKIKNFRKKWWNEFREKLWEAMLSEHKNNINNCKNIPQEELQITQWIKEWHGEFLLERDNRSKLKECIDPCMKYRDWIIRSKFEWHTLSKEYETQKKVSLLLNNCDAEYSKYC  281
                                    19        29||      41        51        61        71        81        91       101       111       121      |136       146       156       166       176       186       196||     221       231       241  ||   271       281
                                               30|                                                                                            128|                                                            197|                            244|                
                                                33                                                                                             134                                                             213                             265

Chain B from PDB  Type:PROTEIN  Length:257
                                                                                                                                                                                                                                                                                                  
               SCOP domains d4k2ub_ B: automated matches                                                                                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh........eeee....eeeehhhhh..hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhh....hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4k2u B    9 EVLSNCREKRKGMKWDCKKKNYVCIPDRRIQLCIVNLSIIKTYTKETMKDHFIEASKKESQLLLKKNDNKYNSKFCNDLKNSFLDYGHLAMGNDMDFGYSTKAENKIQEVFKISEHKIKNFRKKWWNEFREKLWEAMLSEHKNNINNCKNIPQEELQITQWIKEWHGEFLLERDNRSKLPKSKCKLYEACEKCIDPCMKYRDWIIRSKFEWHTLSKEYETQKVPKENAENYLIKISDAKVSLLLNNCDAEYSKYCDC  283
                                    18        28|       42        52        62        72        82        92       102       113       123 ||    138       148       158       168       178       188       198    || 211 ||    222       232       242       252     ||266       276       
                                              28|                                                                          110|          125|                                                                     203|   213|                                        258|                    
                                               33                                                                           112           131                                                                      207    215                                         263

Chain H from PDB  Type:PROTEIN  Length:208
                                                                                                                                                                                                                                                 
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee......eeeeeee..hhhhh.eeeeee...eeeeee......eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeee........eeee...eeeee........eeeee...eeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeee.hhhhh.....eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4k2u H    1 EVQLQQSGAELVKPGASVKLSCTASGFNIKDNYMHWVKQRPLEWIGRIDPANGNTKYDPKFQGKATITADTSSNTAYLQLSSLTSEDTAVYYCARHYDGYFLYYFEYWGQGTTLTVSSAKTTPPSVYPLAPVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVP  212
                                    10        20        30        40||     52A        62        72        82|||     89        99 ||||  105       115       125||     144       154       164       174       184       194       204        
                                                                   41|     52A                            82A||               100A|||                       126|                                                                            
                                                                    45                                     82B|                100B||                        136                                                                            
                                                                                                            82C                 100C|                                                                                                       
                                                                                                                                 100D

Chain I from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                       
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeee........eeee...eeeee........eeeee...eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.hhh.....eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4k2u I    1 EVQLQQSGAELVKPGASVKLSCTASGFNIKDNYMHWVKQRPEQGLEWIGRIDPANGNTKYDPKFQGKATITADTSSNTAYLQLSSLTSEDTAVYYCARHYDGYFLYYFEYWGQGTTLTVSSAKTTPPSVYPLAPSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPR  213
                                    10        20        30        40        50  |     59        69        79   |||  86        96    |||102       112       122   ||  139       149       159       169       179       189       199       209    
                                                                              52A                            82A||               100A|||                       126|                                                                               
                                                                                                              82B|                100B||                        134                                                                               
                                                                                                               82C                 100C|                                                                                                          
                                                                                                                                    100D

Chain L from PDB  Type:PROTEIN  Length:208
                                                                                                                                                                                                                                                 
               SCOP domains d4k2ul1 L:1-107 automated matches                                                                          d4k2ul2 L:108-210 automated matches                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee....eeee.....eeeeeee.......eeeeee.....eeeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeee.......eeeeee..........ee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4k2u L    1 DIQMTQTTSSLSASLGDRVTITCRAGQDISNYLNWYQQKPDGTVKLLIYYTSRLHSGVPSRFSGSGSGTDYSLTISNLEQEDIATYFCQQGSTFPWTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYHNSYTCEATHKKGEFQHTGGRY  210
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180     ||192       202        
                                                                                                                                                                                                                   186|                     
                                                                                                                                                                                                                    189

Chain M from PDB  Type:PROTEIN  Length:200
                                                                                                                                                                                                                                         
               SCOP domains d4k2um1 M:1-107 automated matches                                                                          d4k2um2 M:108-200 automated matches                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee....eeeee....eeeeeee.......eeeeee.....eeeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeeee......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee...ee...eeeee.........eeeeeeeeeehhhhhhh..eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4k2u M    1 DIQMTQTTSSLSASLGDRVTITCRAGQDISNYLNWYQQKPDGTVKLLIYYTSRLHSGVPSRFSGSGSGTDYSLTISNLEQEDIATYFCQQGSTFPWTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKK  200
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ 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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: Duffy binding domain-like (7)

Superfamily: Duffy binding domain-like (7)

Family: automated matches (1)

Protein domain: automated matches (1)

Plasmodium falciparum [TaxId: 36329] (1)

1a	d4k2ua_	A:
1b	d4k2ub_	B:

Class: All beta proteins (24004)

Fold: Immunoglobulin-like beta-sandwich (7299)

Superfamily: Immunoglobulin (5995)

Family: automated matches (864)

Protein domain: automated matches (864)

Mouse (Mus musculus) [TaxId: 10090] (360)

2a	d4k2ul1	L:1-107
2b	d4k2ul2	L:108-210
2c	d4k2um1	M:1-107
2d	d4k2um2	M:108-200

(no "CATH Domain" information available for 4K2U)

(no "Pfam Domain" information available for 4K2U)

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Cis Peptide Bonds
		Arg L:209 - Tyr L:210	[ RasMol ]
		Glu H:148 - Pro H:149	[ RasMol ]
		Glu I:148 - Pro I:149	[ RasMol ]
		Lys L:199 - Lys L:200	[ RasMol ]
		Phe H:146 - Pro H:147	[ RasMol ]
		Phe I:146 - Pro I:147	[ RasMol ]
		Phe L:94 - Pro L:95	[ RasMol ]
		Phe M:94 - Pro M:95	[ RasMol ]
		Thr M:7 - Thr M:8	[ RasMol ]
		Trp H:188 - Pro H:189	[ RasMol ]
		Trp I:188 - Pro I:189	[ RasMol ]
		Tyr L:140 - Pro L:141	[ RasMol ]
		Tyr M:140 - Pro M:141	[ RasMol ]

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		Biological Unit 2	[ Jena3D ]

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Description

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Ligands, Modified Residues, Ions (1, 12)

Sites (12, 12)

SS Bonds (17, 17)

Cis Peptide Bonds (13, 13)

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