1HWM - JenaLib

Asym./Biol. Unit - manually (Jmol Viewer)

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   EBULIN,ORTHORHOMBIC CRYSTAL FORM MODEL

Authors :   J. M. Pascal, P. J. Day, A. F. Monzingo, S. R. Ernst, J. D. Robertus

Date :   09 Jan 01 (Deposition) - 24 Jan 01 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

Chains :   Asym./Biol. Unit : A,B

Keywords :   Ribosome-Inactivating Protein, Ricin-Like, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. M. Pascal, P. J. Day, A. F. Monzingo, S. R. Ernst, J. D. Robertus, R. Iglesias, Y. Perez, J. M. Ferreras, L. Citores, T. Girbes
2. 8-A Crystal Structure Of A Nontoxic Type-Ii Ribosome-Inactivating Protein, Ebulin L.
Proteins V. 43 319 2001
PubMed-ID: 11288182 | Reference-DOI: 10.1002/PROT.1043

Molecule 1 - EBULIN
	Chains	:	A
	EC Number	:	3.2.2.22
	Organism Scientific	:	SAMBUCUS EBULUS
	Organism Taxid	:	28503
	Other Details	:	N-GLYCOSIDASE
	Synonym	:	EBULIN A CHAIN
	Tissue	:	LEAF

Molecule 2 - EBULIN
	Chains	:	B
	EC Number	:	3.2.2.22
	Organism Scientific	:	SAMBUCUS EBULUS
	Organism Taxid	:	28503
	Other Details	:	GALACTOSIDE SPECIFIC LECTIN
	Synonym	:	EBULIN B CHAIN
	Tissue	:	LEAF

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 6)

No.	Name	Count	Type	Full Name
1	BMA	2	Ligand/Ion	BETA-D-MANNOSE
2	GAL	1	Ligand/Ion	BETA-D-GALACTOSE
3	MAN	1	Ligand/Ion	ALPHA-D-MANNOSE
4	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN B:174 , ASN B:186 , ARG B:189 , NAG B:268	BINDING SITE FOR RESIDUE NAG B 267
2	AC2	SOFTWARE	NAG B:267 , BMA B:269	BINDING SITE FOR RESIDUE NAG B 268
3	AC3	SOFTWARE	NAG B:268 , BMA B:270 , MAN B:271	BINDING SITE FOR RESIDUE BMA B 269
4	AC4	SOFTWARE	BMA B:269	BINDING SITE FOR RESIDUE BMA B 270
5	AC5	SOFTWARE	ASP A:65 , BMA B:269	BINDING SITE FOR RESIDUE MAN B 271
6	AC6	SOFTWARE	ASP B:24 , VAL B:25 , ARG B:26 , ASN B:27 , GLN B:37 , TRP B:39 , ARG B:115	BINDING SITE FOR RESIDUE GAL B 280

Asymmetric/Biological Unit

No.	Residues
1	A:249	-	B:5
2	B:22	-	B:41
3	B:63	-	B:80
4	B:151	-	B:166
5	B:192	-	B:209

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

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

(no "PROSITE Motif" information available for 1HWM)

(no "Exon" information available for 1HWM)

Asymmetric/Biological 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:251
 aligned with Q9AVR2_SAMEB | Q9AVR2 from UniProtKB/TrEMBL  Length:564

    Alignment length:251
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275 
         Q9AVR2_SAMEB    26 IDYPSVSFNLAGAKSTTYRDFLKNLRDRVATGTYEVNGLPVLRRESEVQVKNRFVLVRLTNYNGDTVTSAVDVTNLYLVAFSANGNSYFFKDATELQKSNLFLGTTQHTLSFTGNYDNLETAAGTRRESIELGPNPLDGAITSLWYDGGVARSLLVLIQMVPEAARFRYIEQEVRRSLQQLTSFTPNALMLSMENNWSSMSLEVQLSGDNVSPFSGTVQLQNYDHTPRLVDNFEELYKITGIAILLFRCVA 276
               SCOP domains d1hwma_ A: Ebulin A-chain                                                                                                                                                                                                                                   SCOP domains
               CATH domains -1hwmA01 A:2-165 Ricin (A subunit), domain 1                                                                                                                         1hwmA02 A:166-251 Ricin (A Subunit), domain 2                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee....hhhhhhhhhhhhhhhhh....ee..ee........hhhh.eeeeeee.....eeeeeee.....eeeeee..eeee....hhhhhhhh....eeee.....hhhhhhhhhh.hhhhh..hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh....eeeeeeeee.....eeeeeehhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1hwm A   1 IDYPSVSFNLAGAKSTTYRDFLKNLRDRVATGTYEVNGLPVLRRESEVQVKNRFVLVRLTNYNGDTVTSAVDVTNLYLVAFSANGNSYFFKDATELQKSNLFLGTTQHTLSFTGNYDNLETAAGTRRESIELGPNPLDGAITSLWYDGGVARSLLVLIQMVPEAARFRYIEQEVRRSLQQLTSFTPNALMLSMENNWSSMSLEVQLSGDNVSPFSGTVQLQNYDHTPRLVDNFEELYKITGIAILLFRCVA 251
                                    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

Chain B from PDB  Type:PROTEIN  Length:264
 aligned with Q9AVR2_SAMEB | Q9AVR2 from UniProtKB/TrEMBL  Length:564

    Alignment length:264
                                   310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560    
         Q9AVR2_SAMEB   301 ETCAIPAPFTRRIVGRDGLCVDVRNGYDTDGTPIQLWPCGTQRNQQWTFYNDKTIRSMGKCMTANGLNSGSYIMITDCSTAAEDATKWEVLIDGSIINPSSGLVMTAPSGASRTTLLLENNIHAASQGWTVSNDVQPIATLIVGYNEMCLQANGENNNVWMEDCDVTSVQQQWALFDDRTIRVNNSRGLCVTSNGYVSKDLIVIRKCQGLATQRWFFNSDGSVVNLKSTRVMDVKESDVSLQEVIIFPATGNPNQQWRTQVPQI 564
               SCOP domains d1hwmb1 B:3-135 Plant cytotoxin B-chain (lectin)                                                                                     d1hwmb2 B:136-266 Plant cytotoxin B-chain (lectin)                                                                                  SCOP domains
               CATH domains 1hwmB01 B:3-138  [code=2.80.10.50, no name defined]                                                                                     1hwmB02 B:139-263  [code=2.80.10.50, no name defined]                                                                        --- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........eeeeeehhhhhee...hhh......eeee....hhhhheee.....eee..eeeee........eeee............eee...eee......eee..........eee....hhhhh.eee.....eeeeeee...eeeeee..eeeeeeee....hhhh.eee.....eee..eeeeeeee......eeeeeee...hhhhh.ee.....ee......eeee.........eeee....hhhh.eeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1hwm B   3 ETCAIPAPFTRRIVGRDGLCVDVRNGYDTDGTPIQLWPCGTQRNQQWTFYNDKTIRSMGKCMTANGLNSGSYIMITDCSTAAEDATKWEVLIDGSIINPSSGLVMTAPSGASRTTLLLENNIHAASQGWTVSNDVQPIATLIVGYNEMCLQANGENNNVWMEDCDVTSVQQQWALFDDRTIRVNNSRGLCVTSNGYVSKDLIVIRKCQGLATQRWFFNSDGSVVNLKSTRVMDVKESDVSLQEVIIFPATGNPNQQWRTQVPQI 266
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: beta-Trefoil (385)

Superfamily: Ricin B-like lectins (91)

Family: Ricin B-like (65)

Protein domain: Plant cytotoxin B-chain (lectin) (21)

Sambucus ebulus, ebulin [TaxId: 28503] (4)

1a	d1hwmb1	B:3-135
1b	d1hwmb2	B:136-266

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: Ebulin A-chain (4)

Sambucus ebulus [TaxId: 28503] (4)

d1hwma_

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (Q9AVR2_SAMEB | Q9AVR2)

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:0016798	hydrolase activity, acting on glycosyl bonds	Catalysis of the hydrolysis of any glycosyl bond.
	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:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	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/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1hwm)

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	1hwm
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(no "Related Entries Specified in the PDB File" available for 1HWM)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 6)

Sites (6, 6)

SS Bonds (5, 5)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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