3LE7 - JenaLib

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Title :   CRYSTAL STRUCTURE OF PD-L1 FROM P. DIOICA IN COMPLEX WITH ADENINE

Authors :   A. Ruggiero, R. Berisio

Date :   14 Jan 10 (Deposition) - 14 Apr 10 (Release) - 14 Apr 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.65

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Ribosome, Adenine, Disulfide Bond, Glycoprotein, Hydrolase, Plant Defense, Protein Synthesis Inhibitor, Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   V. Severino, A. Chambery, A. Di Maro, D. Marasco, A. Ruggiero, R. Berisio, F. Giansanti, R. Ippoliti, A. Parente
The Role Of The Glycan Moiety On The Structure-Function Relationships Of Pd-L1, Type 1 Ribosome-Inactivating Protein From P. Dioica Leaves
Mol Biosyst V. 6 570 2010
PubMed-ID: 20174685 | Reference-DOI: 10.1039/B919801F

Molecule 1 - RIBOSOME-INACTIVATING PROTEIN PD-L1/PD-L2
	Chains	:	A, B
	EC Number	:	3.2.2.22
	Organism Common	:	BELLA SOMBRA TREE
	Organism Scientific	:	PHYTOLACCA DIOICA
	Organism Taxid	:	29725
	Synonym	:	RRNA N-GLYCOSIDASE PD-L1/PD-L2

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 5)

No.	Name	Count	Type	Full Name
1	ADE	2	Ligand/Ion	ADENINE
2	NAG	3	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	ADE	1	Ligand/Ion	ADENINE
2	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	ADE	1	Ligand/Ion	ADENINE
2	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:13 , HOH A:392 , HOH A:437 , HOH A:442 , HOH A:514 , HOH A:584 , HOH A:592 , HOH A:602 , HOH A:608 , HOH A:614 , NAG B:2	BINDING SITE FOR RESIDUE NAG A 3
2	AC2	SOFTWARE	ASN A:72 , ASN A:73 , TYR A:75 , GLU A:208 , TRP A:210 , GLY A:211 , ASN A:255 , HOH A:276 , HOH A:293 , HOH A:523 , HOH A:524 , HOH A:530	BINDING SITE FOR RESIDUE NAG A 265
3	AC3	SOFTWARE	LEU A:74 , TYR A:75 , VAL A:76 , PHE A:92 , SER A:123 , TYR A:125 , ILE A:173 , SER A:177 , GLU A:178 , ARG A:181 , HOH A:483 , HOH A:590	BINDING SITE FOR RESIDUE ADE A 501
4	AC4	SOFTWARE	NAG A:3 , ASN B:13 , HOH B:433 , HOH B:446 , HOH B:453 , HOH B:628	BINDING SITE FOR RESIDUE NAG B 2
5	AC5	SOFTWARE	LEU B:74 , TYR B:75 , VAL B:76 , PHE B:92 , SER B:123 , TYR B:125 , ILE B:173 , SER B:177 , GLU B:178 , ARG B:181 , HOH B:456 , HOH B:568	BINDING SITE FOR RESIDUE ADE B 601

Asymmetric Unit

No.	Residues
1	A:37	-	A:261
2	A:87	-	A:108
3	B:37	-	B:261
4	B:87	-	B:108

(no "Cis Peptide Bond" information available for 3LE7)

(no "SAP(SNP)/Variant" information available for 3LE7)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SHIGA_RICIN	PS00275	Shiga/ricin ribosomal inactivating toxins active site signature.	RIPL1_PHYDI	170-186	2	A:173-189 B:173-189

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SHIGA_RICIN	PS00275	Shiga/ricin ribosomal inactivating toxins active site signature.	RIPL1_PHYDI	170-186	1	A:173-189 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SHIGA_RICIN	PS00275	Shiga/ricin ribosomal inactivating toxins active site signature.	RIPL1_PHYDI	170-186	1	- B:173-189

(no "Exon" information available for 3LE7)

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
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Chain A from PDB  Type:PROTEIN  Length:261
 aligned with RIPL1_PHYDI | P84853 from UniProtKB/Swiss-Prot  Length:261

    Alignment length:261
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260 
          RIPL1_PHYDI     1 INTITYDAGNTTINKYATFMESLRNEAKDPSLQCYGIPMLPNNSSTIKYLLVKLQGASQKTITLMLRRNNLYVMGYSDPFNGNCRYHIFNDITGTERTNVENTLCSSSSSRDAKPINYNSLYSTLEKKAEVNSRSQVQLGIQILSSDIGKISGQSSFTDKTEAKFLLVAIQMVSEAARFKYIENQVKTNFNRDFSPNDKILDLEENWGKISTAIHDATNGALPKPLELKNADGTKWIVLRVDEIKPDMGLLNYVNGTCQTT 261
               SCOP domains d3le7a_ A: automated matches                                                                                                                                                                                                                                          SCOP domains
               CATH domains 3le7A01 A:4-180 Ricin (A subunit), domain 1                                                                                                                                      3le7A02 A:181-261 Ricin (A Subunit), domain 2                                    --- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhhhhhhhh....ee..ee..........eeeeeee.hhh.eeeeeee.....eeeeeeee..eeeeee.....hhhhhhhhhhhh.....eee.......hhhhhhhhh...hhhhh..hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh....eeeeeeeee.....eeeeeehhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------SHIGA_RICIN      --------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3le7 A   4 INTITYDAGNTTINKYATFMESLRNEAKDPSLQCYGIPMLPNNSSTIKYLLVKLQGASQKTITLMLRRNNLYVMGYSDPFNGNCRYHIFNDITGTERTNVENTLCSSSSSRDAKPINYNSLYSTLEKKAEVNSRSQVQLGIQILSSDIGKISGQSSFTDKTEAKFLLVAIQMVSEAARFKYIENQVKTNFNRDFSPNDKILDLEENWGKISTAIHDATNGALPKPLELKNADGTKWIVLRVDEIKPDMGLLNYVNGTCQTT 264
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263

Chain B from PDB  Type:PROTEIN  Length:261
 aligned with RIPL1_PHYDI | P84853 from UniProtKB/Swiss-Prot  Length:261

    Alignment length:261
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260 
          RIPL1_PHYDI     1 INTITYDAGNTTINKYATFMESLRNEAKDPSLQCYGIPMLPNNSSTIKYLLVKLQGASQKTITLMLRRNNLYVMGYSDPFNGNCRYHIFNDITGTERTNVENTLCSSSSSRDAKPINYNSLYSTLEKKAEVNSRSQVQLGIQILSSDIGKISGQSSFTDKTEAKFLLVAIQMVSEAARFKYIENQVKTNFNRDFSPNDKILDLEENWGKISTAIHDATNGALPKPLELKNADGTKWIVLRVDEIKPDMGLLNYVNGTCQTT 261
               SCOP domains d3le7b_ B: automated matches                                                                                                                                                                                                                                          SCOP domains
               CATH domains 3le7B01 B:4-180 Ricin (A subunit), domain 1                                                                                                                                      3le7B02 B:181-261 Ricin (A Subunit), domain 2                                    --- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhhhhhhhh....ee..ee..........eeeeeee.hhh.eeeeeee.....eeeeeeee..eeeeee....hhhhhhhhhhhhh.....eee.......hhhhhhhhh...hhhhh..hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh...eeeeeeeee.....eeeeeehhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------SHIGA_RICIN      --------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3le7 B   4 INTITYDAGNTTINKYATFMESLRNEAKDPSLQCYGIPMLPNNSSTIKYLLVKLQGASQKTITLMLRRNNLYVMGYSDPFNGNCRYHIFNDITGTERTNVENTLCSSSSSRDAKPINYNSLYSTLEKKAEVNSRSQVQLGIQILSSDIGKISGQSSFTDKTEAKFLLVAIQMVSEAARFKYIENQVKTNFNRDFSPNDKILDLEENWGKISTAIHDATNGALPKPLELKNADGTKWIVLRVDEIKPDMGLLNYVNGTCQTT 264
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263

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: Alpha and beta proteins (a+b) (23004)

Fold: Ribosome inactivating proteins (RIP) (180)

Superfamily: Ribosome inactivating proteins (RIP) (180)

Family: Plant cytotoxins (166)

Protein domain: automated matches (73)

Phytolacca dioica [TaxId: 29725] (6)

1a	d3le7a_	A:
1b	d3le7b_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Ricin (A subunit); domain 1 (112)

Homologous Superfamily: Ricin (A subunit), domain 1 (112)

Bella sombra tree (Phytolacca dioica) (2)

1a	3le7A01	A:4-180
1b	3le7B01	B:4-180

Class: Few Secondary Structures (1120)

Architecture: Irregular (1120)

Topology: Ricin (A Subunit), domain 2 (112)

Homologous Superfamily: Ricin (A Subunit), domain 2 (112)

Bella sombra tree (Phytolacca dioica) (2)

2a	3le7A02	A:181-261
2b	3le7B02	B:181-261

(no "Pfam Domain" information available for 3LE7)

Asymmetric Unit(hide GO term definitions)

Chain A,B (RIPL1_PHYDI | P84853)

molecular function
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0030598	rRNA N-glycosylase activity	Catalysis of the hydrolysis of the N-glycosylic bond at A-4324 in 28S rRNA from rat ribosomes or corresponding sites in 28S RNA from other species.
biological process
	GO:0006952	defense response	Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.
	GO:0017148	negative regulation of translation	Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.

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	RIPL1_PHYDI \| P84853	:	3h5k

3h5k	CRYSTAL STRUCTURE OF PD-L1 FROM P. DIOICA

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 5)

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SS Bonds (4, 4)

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