1CF5 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   BETA-MOMORCHARIN STRUCTURE AT 2.55 A

Authors :   Y. -R. Yuan, Y. -N. He, J. -P. Xiong, Z. -X. Xia

Date :   24 Mar 99 (Deposition) - 07 Jun 99 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.55

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

Keywords :   Ribosome-Inactivating Protein, Rna N-Glycosidase Activity, Glycoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. R. Yuan, Y. N. He, J. P. Xiong, Z. X. Xia
Three-Dimensional Structure Of Beta-Momorcharin At 2. 55 A Resolution.
Acta Crystallogr. , Sect. D V. 55 1144 1999
PubMed-ID: 10329776 | Reference-DOI: 10.1107/S0907444999003297
(for further references see the PDB file header)

Molecule 1 - PROTEIN (BETA-MOMORCHARIN)
	Chains	:	A, B
	Organism Common	:	BALSAM PEAR
	Organism Scientific	:	MOMORDICA CHARANTIA
	Organism Taxid	:	3673

		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 (5, 12)

No.	Name	Count	Type	Full Name
1	BMA	2	Ligand/Ion	BETA-D-MANNOSE
2	FUC	2	Ligand/Ion	ALPHA-L-FUCOSE
3	MAN	2	Ligand/Ion	ALPHA-D-MANNOSE
4	NAG	4	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
5	XYP	2	Ligand/Ion	BETA-D-XYLOPYRANOSE

Biological Unit 1 (5, 6)

No.	Name	Count	Type	Full Name
1	BMA	1	Ligand/Ion	BETA-D-MANNOSE
2	FUC	1	Ligand/Ion	ALPHA-L-FUCOSE
3	MAN	1	Ligand/Ion	ALPHA-D-MANNOSE
4	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
5	XYP	1	Ligand/Ion	BETA-D-XYLOPYRANOSE

Biological Unit 2 (5, 6)

No.	Name	Count	Type	Full Name
1	BMA	1	Ligand/Ion	BETA-D-MANNOSE
2	FUC	1	Ligand/Ion	ALPHA-L-FUCOSE
3	MAN	1	Ligand/Ion	ALPHA-D-MANNOSE
4	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
5	XYP	1	Ligand/Ion	BETA-D-XYLOPYRANOSE

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLU A:248 , NAG A:902 , NAG A:903	BINDING SITE FOR RESIDUE FUC A 901
02	AC2	SOFTWARE	ASP A:1 , ASN A:3 , ASN A:51 , THR A:53 , FUC A:901 , NAG A:903	BINDING SITE FOR RESIDUE NAG A 902
03	AC3	SOFTWARE	TYR A:57 , GLU A:248 , FUC A:901 , NAG A:902 , BMA A:904	BINDING SITE FOR RESIDUE NAG A 903
04	AC4	SOFTWARE	GLU A:248 , ASN A:249 , NAG A:903 , MAN A:905 , XYP A:906	BINDING SITE FOR RESIDUE BMA A 904
05	AC5	SOFTWARE	GLU A:110 , ASN A:188 , BMA A:904	BINDING SITE FOR RESIDUE MAN A 905
06	AC6	SOFTWARE	ASN A:209 , PRO A:210 , ASN A:249 , BMA A:904	BINDING SITE FOR RESIDUE XYP A 906
07	AC7	SOFTWARE	GLU B:248 , NAG B:902 , NAG B:903	BINDING SITE FOR RESIDUE FUC B 901
08	AC8	SOFTWARE	ASN B:3 , ASP B:5 , ASN B:51 , THR B:53 , FUC B:901 , NAG B:903	BINDING SITE FOR RESIDUE NAG B 902
09	AC9	SOFTWARE	FUC B:901 , NAG B:902 , BMA B:904 , XYP B:906	BINDING SITE FOR RESIDUE NAG B 903
10	BC1	SOFTWARE	NAG B:903 , MAN B:905 , XYP B:906	BINDING SITE FOR RESIDUE BMA B 904
11	BC2	SOFTWARE	ASN B:188 , GLN B:189 , BMA B:904	BINDING SITE FOR RESIDUE MAN B 905
12	BC3	SOFTWARE	GLN B:189 , ASN B:209 , PRO B:210 , NAG B:903 , BMA B:904 , HOH B:909	BINDING SITE FOR RESIDUE XYP B 906

(no "SS Bond" information available for 1CF5)

(no "Cis Peptide Bond" information available for 1CF5)

(no "SAP(SNP)/Variant" information available for 1CF5)

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.	RIP3_MOMCH	176-192	2	A:153-169 B:153-169
1	SHIGA_RICIN	PS00275		RIP2_MOMBA	176-192	2	A:153-169 B:153-169

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.	RIP3_MOMCH	176-192	1	A:153-169 -
1	SHIGA_RICIN	PS00275		RIP2_MOMBA	176-192	1	A:153-169 -

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.	RIP3_MOMCH	176-192	1	- B:153-169
1	SHIGA_RICIN	PS00275		RIP2_MOMBA	176-192	1	- B:153-169

(no "Exon" information available for 1CF5)

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:249
 aligned with RIP2_MOMBA | P29339 from UniProtKB/Swiss-Prot  Length:286

    Alignment length:249
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263         
           RIP2_MOMBA    24 DVNFDLSTATAKTYTKFIEDFRATLPFSHKVYDIPLLYSTISDSRRFILLDLTSYAYETISVAIDVTNVYVVAYRTRDVSYFFKESPPEAYNILFKGTRKITLPYTGNYENLQTAAHKIRENIDLGLPALSSAITTLFYYNAQSAPSALLVLIQTTAEAARFKYIERHVAKYVATNFKPNLAIISLENQWSALSKQIFLAQNQGGKFRNPVDLIKPTGERFQVTNVDSDVVKGNIKLLLNSRASTADEN 272
               SCOP domains d1cf5a_ A: Beta-momorcharin                                                                                                                                                                                                                               SCOP domains
               CATH domains 1cf5A01 A:1-160 Ricin (A subunit), domain 1                                                                                                                     1cf5A02 A:161-246 Ricin (A Subunit), domain 2                                         --- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
     Sec.struct. author (1) .eeeee...hhhhhhhhhhhhhhh...eeee..eee.....hhhhh--------..eeeeeeeeee.eeeeeeeee..eeeeee...hhhhhhh....eeeee....hhhhhhhhhh.hhhhh..hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhh..........eeeee..eeeeee....hhhhhhh.....hhhhhh.... Sec.struct. author (1)
     Sec.struct. author (2) ---------------------------------------------eeeeeeeee--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Sec.struct. author (2)
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------------------------SHIGA_RICIN      -------------------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1cf5 A   1 DVNFDLSTATAKTYTKFIEDFRATLPFSHKVYDIPLLYSTISDSRRFILLNLTSYAYETISVAIDVTNVYVVAYRTRDVSYFFKESPPEAYNILFKGTRKITLPYTGNYENLQTAAHKIRENIDLGLPALSSAITTLFYYNAQSAPSALLVLIQTTAEAARFKYIERHVAKYVATNFKPNLAIISLENQWSALSKQIFLAQNQGGKFRNPVDLIKPTGQRFQVTNVDSDVVKGNIKLLLNSRASTADEN 249
                                    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:249
 aligned with RIP3_MOMCH | P24817 from UniProtKB/Swiss-Prot  Length:286

    Alignment length:249
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263         
           RIP3_MOMCH    24 DVNFDLSTATAKTYTKFIEDFRATLPFSHKVYDIPLLYSTISDSRRFILLNLTSYAYETISVAIDVTNVYVVAYRTRDVSYFFKESPPEAYNILFKGTRKITLPYTGNYENLQTAAHKIRENIDLGLPALSSAITTLFYYNAQSAPSALLVLIQTTAEAARFKYIERHVAKYVATNFKPNLAIISLENQWSALSKQIFLAQNQGGKFRNPVDLIKPTGERFQVTNVDSDVVKGNIKLLLNSRASTADEN 272
               SCOP domains d1cf5a_ A: Beta-momorcharin                                                                                                                                                                                                                               SCOP domains
               CATH domains 1cf5A01 A:1-160 Ricin (A subunit), domain 1                                                                                                                     1cf5A02 A:161-246 Ricin (A Subunit), domain 2                                         --- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
     Sec.struct. author (1) .eeeee...hhhhhhhhhhhhhhh...eeee..eee.....hhhhh--------..eeeeeeeeee.eeeeeeeee..eeeeee...hhhhhhh....eeeee....hhhhhhhhhh.hhhhh..hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhh..........eeeee..eeeeee....hhhhhhh.....hhhhhh.... Sec.struct. author (1)
     Sec.struct. author (2) ---------------------------------------------eeeeeeeee--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Sec.struct. author (2)
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------SHIGA_RICIN      -------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1cf5 A   1 DVNFDLSTATAKTYTKFIEDFRATLPFSHKVYDIPLLYSTISDSRRFILLNLTSYAYETISVAIDVTNVYVVAYRTRDVSYFFKESPPEAYNILFKGTRKITLPYTGNYENLQTAAHKIRENIDLGLPALSSAITTLFYYNAQSAPSALLVLIQTTAEAARFKYIERHVAKYVATNFKPNLAIISLENQWSALSKQIFLAQNQGGKFRNPVDLIKPTGQRFQVTNVDSDVVKGNIKLLLNSRASTADEN 249
                                    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:249
 aligned with RIP2_MOMBA | P29339 from UniProtKB/Swiss-Prot  Length:286

    Alignment length:249
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263         
           RIP2_MOMBA    24 DVNFDLSTATAKTYTKFIEDFRATLPFSHKVYDIPLLYSTISDSRRFILLDLTSYAYETISVAIDVTNVYVVAYRTRDVSYFFKESPPEAYNILFKGTRKITLPYTGNYENLQTAAHKIRENIDLGLPALSSAITTLFYYNAQSAPSALLVLIQTTAEAARFKYIERHVAKYVATNFKPNLAIISLENQWSALSKQIFLAQNQGGKFRNPVDLIKPTGERFQVTNVDSDVVKGNIKLLLNSRASTADEN 272
               SCOP domains d1cf5b_ B: Beta-momorcharin                                                                                                                                                                                                                               SCOP domains
               CATH domains 1cf5B01 B:1-160 Ricin (A subunit), domain 1                                                                                                                     1cf5B02 B:161-246 Ricin (A Subunit), domain 2                                         --- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
     Sec.struct. author (1) .eeeee...hhhhhhhhhhhhhhh...eeee..eee.....hhhhh--------..eeeeeeeeee.eeeeeeeee..eeeeee...hhhhhhh....eeeee....hhhhhhhhhh.hhhhh..hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhh..........eeeee..eeeeee....hhhhhhh.....hhhhhh.... Sec.struct. author (1)
     Sec.struct. author (2) ---------------------------------------------eeeeeeeee--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Sec.struct. author (2)
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------------------------SHIGA_RICIN      -------------------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1cf5 B   1 DVNFDLSTATAKTYTKFIEDFRATLPFSHKVYDIPLLYSTISDSRRFILLNLTSYAYETISVAIDVTNVYVVAYRTRDVSYFFKESPPEAYNILFKGTRKITLPYTGNYENLQTAAHKIRENIDLGLPALSSAITTLFYYNAQSAPSALLVLIQTTAEAARFKYIERHVAKYVATNFKPNLAIISLENQWSALSKQIFLAQNQGGKFRNPVDLIKPTGQRFQVTNVDSDVVKGNIKLLLNSRASTADEN 249
                                    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:249
 aligned with RIP3_MOMCH | P24817 from UniProtKB/Swiss-Prot  Length:286

    Alignment length:249
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263         
           RIP3_MOMCH    24 DVNFDLSTATAKTYTKFIEDFRATLPFSHKVYDIPLLYSTISDSRRFILLNLTSYAYETISVAIDVTNVYVVAYRTRDVSYFFKESPPEAYNILFKGTRKITLPYTGNYENLQTAAHKIRENIDLGLPALSSAITTLFYYNAQSAPSALLVLIQTTAEAARFKYIERHVAKYVATNFKPNLAIISLENQWSALSKQIFLAQNQGGKFRNPVDLIKPTGERFQVTNVDSDVVKGNIKLLLNSRASTADEN 272
               SCOP domains d1cf5b_ B: Beta-momorcharin                                                                                                                                                                                                                               SCOP domains
               CATH domains 1cf5B01 B:1-160 Ricin (A subunit), domain 1                                                                                                                     1cf5B02 B:161-246 Ricin (A Subunit), domain 2                                         --- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
     Sec.struct. author (1) .eeeee...hhhhhhhhhhhhhhh...eeee..eee.....hhhhh--------..eeeeeeeeee.eeeeeeeee..eeeeee...hhhhhhh....eeeee....hhhhhhhhhh.hhhhh..hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhh..........eeeee..eeeeee....hhhhhhh.....hhhhhh.... Sec.struct. author (1)
     Sec.struct. author (2) ---------------------------------------------eeeeeeeee--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Sec.struct. author (2)
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------SHIGA_RICIN      -------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1cf5 B   1 DVNFDLSTATAKTYTKFIEDFRATLPFSHKVYDIPLLYSTISDSRRFILLNLTSYAYETISVAIDVTNVYVVAYRTRDVSYFFKESPPEAYNILFKGTRKITLPYTGNYENLQTAAHKIRENIDLGLPALSSAITTLFYYNAQSAPSALLVLIQTTAEAARFKYIERHVAKYVATNFKPNLAIISLENQWSALSKQIFLAQNQGGKFRNPVDLIKPTGQRFQVTNVDSDVVKGNIKLLLNSRASTADEN 249
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	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: Beta-momorcharin (2)

Bitter gourd (Momordica charantia) [TaxId: 3673] (2)

1a	d1cf5a_	A:
1b	d1cf5b_	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)

Balsam pear (Momordica charantia) (9)

1a	1cf5A01	A:1-160
1b	1cf5B01	B:1-160

Class: Few Secondary Structures (1120)

Architecture: Irregular (1120)

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

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

Balsam pear (Momordica charantia) (9)

2a	1cf5A02	A:161-246
2b	1cf5B02	B:161-246

(no "Pfam Domain" information available for 1CF5)

Asymmetric Unit(hide GO term definitions)

Chain A,B (RIP2_MOMBA | P29339)

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 (RIP3_MOMCH | P24817)

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.
	GO:0050688	regulation of defense response to virus	Any process that modulates the frequency, rate or extent of the antiviral response of a cell or organism.

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	1cf5
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(no "Related Entries Specified in the PDB File" available for 1CF5)

Description

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Ligands, Modified Residues, Ions (5, 12)

Sites (12, 12)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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