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Title :   X-RAY SEQUENCE AND CRYSTAL STRUCTURE OF LUFFACULIN 1, A NOVEL TYPE 1 RIBOSOME-INACTIVATING PROTEIN

Authors :   X. Hou, M. Huang

Date :   31 Jan 07 (Deposition) - 29 May 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.40

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

Keywords :   Mixed Alpha Helix And Beta Sheet, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   X. Hou, M. Chen, L. Chen, E. J. Meehan, J. Xie, M. Huang
X-Ray Sequence And Crystal Structure Of Luffaculin 1, A Novel Type 1 Ribosome-Inactivating Protein
Bmc Struct. Biol. V. 7 29 2007
PubMed-ID: 17470286 | Reference-DOI: 10.1186/1472-6807-7-29

Molecule 1 - LUFFACULIN 1
	Chains	:	A, B
	Organism Scientific	:	LUFFA ACUTANGULA
	Organism Taxid	:	56866
	Tissue	:	SEED

		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 (3, 7)

No.	Name	Count	Type	Full Name
1	NAG	4	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
2	PEG	2	Ligand/Ion	DI(HYDROXYETHYL)ETHER
3	PG4	1	Ligand/Ion	TETRAETHYLENE GLYCOL

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
2	PEG	-1	Ligand/Ion	DI(HYDROXYETHYL)ETHER
3	PG4	1	Ligand/Ion	TETRAETHYLENE GLYCOL

Biological Unit 2 (2, 4)

No.	Name	Count	Type	Full Name
1	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
2	PEG	2	Ligand/Ion	DI(HYDROXYETHYL)ETHER
3	PG4	-1	Ligand/Ion	TETRAETHYLENE GLYCOL

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	VAL A:76 , ASN A:77 , TYR A:81 , PHE A:139 , HIS A:140 , HOH A:291 , HOH A:492 , HOH A:502 , HOH A:531 , ASN B:77 , SER B:78 , THR B:79 , NAG B:1002	BINDING SITE FOR RESIDUE NAG A 1001
2	AC2	SOFTWARE	ASN A:77 , SER A:78 , THR A:79 , HOH A:291 , NAG A:1001 , VAL B:76 , ASN B:77 , PHE B:139 , HIS B:140 , HOH B:496 , HOH B:505 , HOH B:509 , HOH B:624	BINDING SITE FOR RESIDUE NAG B 1002
3	AC3	SOFTWARE	LYS A:23 , ALA A:24 , ASN B:84 , PRO B:105 , HOH B:390 , HOH B:404	BINDING SITE FOR RESIDUE NAG B 1003
4	AC4	SOFTWARE	ASN A:84 , GLU A:85 , LYS A:89 , THR A:103 , HOH A:288 , HOH A:300 , HOH A:466	BINDING SITE FOR RESIDUE NAG A 1004
5	AC5	SOFTWARE	ASP A:1 , TYR A:47 , HOH A:332 , HOH A:410 , HOH A:413 , HOH A:585	BINDING SITE FOR RESIDUE PG4 A 801
6	AC6	SOFTWARE	LEU B:75 , PHE B:96 , ALA B:97 , SER B:99 , HOH B:515	BINDING SITE FOR RESIDUE PEG B 802
7	AC7	SOFTWARE	GLU B:190 , ALA B:193 , LYS B:196 , GLN B:197 , PRO B:211	BINDING SITE FOR RESIDUE PEG B 803

(no "SS Bond" information available for 2OQA)

(no "Cis Peptide Bond" information available for 2OQA)

(no "SAP(SNP)/Variant" information available for 2OQA)

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.	RIP_LUFAC	154-170	2	A:154-170 B:154-170
1	SHIGA_RICIN	PS00275		RIPA_LUFAE	174-190	2	A:154-170 B:154-170

Biological Unit 1 (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.	RIP_LUFAC	154-170	1	A:154-170 -
1	SHIGA_RICIN	PS00275		RIPA_LUFAE	174-190	1	A:154-170 -

Biological Unit 2 (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.	RIP_LUFAC	154-170	1	- B:154-170
1	SHIGA_RICIN	PS00275		RIPA_LUFAE	174-190	1	- B:154-170

(no "Exon" information available for 2OQA)

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:241
 aligned with RIPA_LUFAE | Q00465 from UniProtKB/Swiss-Prot  Length:277

    Alignment length:241
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260 
           RIPA_LUFAE    21 DVRFSLSGSSSTSYSKFIGDLRKALPSNGTVYNITLLLSSASGASRYTLMTLSNYDGKAITVAVDVTNVYIMGYLVNSTSYFFNESDAKLASQYVFKGSTIVTLPYSGNYEKLQTAAGKIREKIPLGFPALDSAITTLFHYDSTAAAAAFLVIIQTTAEASRFKYIEGQIIERISKNQVPSLATISLENEWSALSKQIQLAQTNNGTFKTPVVITDDKGQRVEITNVTSKVVTKNIQLLLN 261
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2oqaA01 A:1-161 Ricin (A subunit), domain 1                                                                                                                      2oqaA02 A:162-241 Ricin (A Subunit), domain 2                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee....hhhhhhhhhhhhhhhh.eeeee..eeee....hhhh.eeeeeee.....eeeeeee.....eeeeee..eeee..hhhhhhhh.......eeee.....hhhhhhhhhh.hhhhh..hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh....eeeeeeeee.....eeeeee..hhhhhh...ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------SHIGA_RICIN      ----------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2oqa A   1 DVSFSLSGSSSTSYSKFIGALRKALPSNGTVYNITLLLSSASGASRYTLMKLSNYDGKAITVAIDVTNVYIMGYLVNSTSYFFNESDAKLASQYVFAGSTIVTLPYSGNYEKLQTAAGKIREKIPLGFPALDSAITTLFHYDSTAAAAAFLVIIQTTAESSRFKYIEGQIIMRISKNGVPSLATISLENEWSALSKQIQLAQTNNGTFKTPVVIMDAGGQRVEIGNVGSKVVTKNIQLLLN 241
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240

Chain A from PDB  Type:PROTEIN  Length:241
 aligned with RIP_LUFAC | P84530 from UniProtKB/Swiss-Prot  Length:241

    Alignment length:241
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240 
            RIP_LUFAC     1 DVSFSLSGSSSTSYSKFIGALRKALPSNGTVYNITLLLSSASGASRYTLMKLSNYDGKAITVAIDVTNVYIMGYLVNSTSYFFNESDAKLASQYVFAGSTIVTLPYSGNYEKLQTAAGKIREKIPLGFPALDSAITTLFHYDSTAAAAAFLVIIQTTAESSRFKYIEGQIIMRISKNGVPSLATISLENEWSALSKQIQLAQTNNGTFKTPVVIMDAGGQRVEIGNVGSKVVTKNIQLLLN 241
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2oqaA01 A:1-161 Ricin (A subunit), domain 1                                                                                                                      2oqaA02 A:162-241 Ricin (A Subunit), domain 2                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee....hhhhhhhhhhhhhhhh.eeeee..eeee....hhhh.eeeeeee.....eeeeeee.....eeeeee..eeee..hhhhhhhh.......eeee.....hhhhhhhhhh.hhhhh..hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh....eeeeeeeee.....eeeeee..hhhhhh...ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------SHIGA_RICIN      ----------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2oqa A   1 DVSFSLSGSSSTSYSKFIGALRKALPSNGTVYNITLLLSSASGASRYTLMKLSNYDGKAITVAIDVTNVYIMGYLVNSTSYFFNESDAKLASQYVFAGSTIVTLPYSGNYEKLQTAAGKIREKIPLGFPALDSAITTLFHYDSTAAAAAFLVIIQTTAESSRFKYIEGQIIMRISKNGVPSLATISLENEWSALSKQIQLAQTNNGTFKTPVVIMDAGGQRVEIGNVGSKVVTKNIQLLLN 241
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240

Chain B from PDB  Type:PROTEIN  Length:233
 aligned with RIPA_LUFAE | Q00465 from UniProtKB/Swiss-Prot  Length:277

    Alignment length:241
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260 
           RIPA_LUFAE    21 DVRFSLSGSSSTSYSKFIGDLRKALPSNGTVYNITLLLSSASGASRYTLMTLSNYDGKAITVAVDVTNVYIMGYLVNSTSYFFNESDAKLASQYVFKGSTIVTLPYSGNYEKLQTAAGKIREKIPLGFPALDSAITTLFHYDSTAAAAAFLVIIQTTAEASRFKYIEGQIIERISKNQVPSLATISLENEWSALSKQIQLAQTNNGTFKTPVVITDDKGQRVEITNVTSKVVTKNIQLLLN 261
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2oqaB01 B:1-161 Ricin (A su bunit), domain 1                                                                                                                     2oqaB02 B:162-241 Ricin (A Subunit), domain  2                                   CATH domains
           Pfam domains (1) --RIP-2oqaB01 B:3-201                                                                                                                                                                                    ---- --------      --------------------- Pfam domains (1)
           Pfam domains (2) --RIP-2oqaB02 B:3-201                                                                                                                                                                                    ---- --------      --------------------- Pfam domains (2)
         Sec.struct. author .eeee....hhhhhhhhhhhhhhhh..-.ee..eee.....hhhh.eeeeeee.....eeeeeee.....eeeeee..eeee..hhhhhhhh.......eeee.....hhhhhhhhhh.hhhhh..hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh...-.....ee.------..ee....hhhhhh...ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------SHIGA_RICIN      ----------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2oqa B   1 DVSFSLSGSSSTSYSKFIGALRKALPS-GTVYNITLLLSSASGASRYTLMKLSNYDGKAITVAIDVTNVYIMGYLVNSTSYFFNESDAKLASQYVFAGSTIVTLPYSGNYEKLQTAAGKIREKIPLGFPALDSAITTLFHYDSTAAAAAFLVIIQTTAESSRFKYIEGQIIMRISKNGVPSLATISLENEWSALSKQIQLAQTNN-TFKTPVVI------RVEIGNVGSKVVTKNIQLLLN 241
                                    10        20      | 30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200    | |210   |     -|      230       240 
                                                     27 |                                                                                                                                                                             205 |    214    221                    
                                                       29                                                                                                                                                                               207

Chain B from PDB  Type:PROTEIN  Length:233
 aligned with RIP_LUFAC | P84530 from UniProtKB/Swiss-Prot  Length:241

    Alignment length:241
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240 
            RIP_LUFAC     1 DVSFSLSGSSSTSYSKFIGALRKALPSNGTVYNITLLLSSASGASRYTLMKLSNYDGKAITVAIDVTNVYIMGYLVNSTSYFFNESDAKLASQYVFAGSTIVTLPYSGNYEKLQTAAGKIREKIPLGFPALDSAITTLFHYDSTAAAAAFLVIIQTTAESSRFKYIEGQIIMRISKNGVPSLATISLENEWSALSKQIQLAQTNNGTFKTPVVIMDAGGQRVEIGNVGSKVVTKNIQLLLN 241
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2oqaB01 B:1-161 Ricin (A su bunit), domain 1                                                                                                                     2oqaB02 B:162-241 Ricin (A Subunit), domain  2                                   CATH domains
           Pfam domains (1) --RIP-2oqaB01 B:3-201                                                                                                                                                                                    ---- --------      --------------------- Pfam domains (1)
           Pfam domains (2) --RIP-2oqaB02 B:3-201                                                                                                                                                                                    ---- --------      --------------------- Pfam domains (2)
         Sec.struct. author .eeee....hhhhhhhhhhhhhhhh..-.ee..eee.....hhhh.eeeeeee.....eeeeeee.....eeeeee..eeee..hhhhhhhh.......eeee.....hhhhhhhhhh.hhhhh..hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh...-.....ee.------..ee....hhhhhh...ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------SHIGA_RICIN      ----------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2oqa B   1 DVSFSLSGSSSTSYSKFIGALRKALPS-GTVYNITLLLSSASGASRYTLMKLSNYDGKAITVAIDVTNVYIMGYLVNSTSYFFNESDAKLASQYVFAGSTIVTLPYSGNYEKLQTAAGKIREKIPLGFPALDSAITTLFHYDSTAAAAAFLVIIQTTAESSRFKYIEGQIIMRISKNGVPSLATISLENEWSALSKQIQLAQTNN-TFKTPVVI------RVEIGNVGSKVVTKNIQLLLN 241
                                    10        20      | 30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200    | |210   |     -|      230       240 
                                                     27 |                                                                                                                                                                             205 |    214    221                    
                                                       29                                                                                                                                                                               207

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 '\|'

(no "SCOP Domain" information available for 2OQA)

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)

Luffa acutangula. Organism_taxid: 56866. (1)

1a	2oqaA01	A:1-161
1b	2oqaB01	B:1-161

Class: Few Secondary Structures (1120)

Architecture: Irregular (1120)

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

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

Luffa acutangula. Organism_taxid: 56866. (1)

2a	2oqaA02	A:162-241
2b	2oqaB02	B:162-241

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: RIP] (62)

Family: RIP (62)

Luffa acutangula (Ridged gourd) (Cucumis acutangulus) (1)

1a	RIP-2oqaB01	B:3-201
1b	RIP-2oqaB02	B:3-201

Asymmetric Unit(hide GO term definitions)

Chain A,B (RIP_LUFAC | P84530)

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.

Chain A,B (RIPA_LUFAE | Q00465)

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:0051607	defense response to virus	Reactions triggered in response to the presence of a virus that act to protect the cell or organism.
	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.

Asymmetric Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2oqa)

Biological Units
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Description

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Ligands, Modified Residues, Ions (3, 7)

Sites (7, 7)

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