1HWP - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   EBULIN COMPLEXED WITH PTEROIC ACID, TRIGONAL CRYSTAL FORM

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 :   3.10

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

Keywords :   Ribosome-Inactivating Protein, Ricin-Like, Inhibitor, 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 Unit	:	A	B
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (2x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 6)

No.	Name	Count	Type	Full Name
1	BGC	1	Ligand/Ion	BETA-D-GLUCOSE
2	BMA	1	Ligand/Ion	BETA-D-MANNOSE
3	GAL	1	Ligand/Ion	BETA-D-GALACTOSE
4	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
5	PT1	1	Ligand/Ion	PTEROIC ACID

Biological Unit 1 (5, 6)

No.	Name	Count	Type	Full Name
1	BGC	1	Ligand/Ion	BETA-D-GLUCOSE
2	BMA	1	Ligand/Ion	BETA-D-MANNOSE
3	GAL	1	Ligand/Ion	BETA-D-GALACTOSE
4	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
5	PT1	1	Ligand/Ion	PTEROIC ACID

Biological Unit 2 (5, 12)

No.	Name	Count	Type	Full Name
1	BGC	2	Ligand/Ion	BETA-D-GLUCOSE
2	BMA	2	Ligand/Ion	BETA-D-MANNOSE
3	GAL	2	Ligand/Ion	BETA-D-GALACTOSE
4	NAG	4	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
5	PT1	2	Ligand/Ion	PTEROIC ACID

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP B:24 , VAL B:25 , ARG B:26 , ASN B:27 , GLY B:28 , GLN B:37 , TRP B:39 , GLN B:44 , ASN B:46 , GLN B:47 , BGC B:281	BINDING SITE FOR RESIDUE GAL B 280
2	AC2	SOFTWARE	ASN B:27 , GLY B:28 , ASN B:46 , GAL B:280	BINDING SITE FOR RESIDUE BGC B 281
3	AC3	SOFTWARE	ALA B:141 , GLN B:174 , ASN B:186 , ARG B:189 , NAG B:268	BINDING SITE FOR RESIDUE NAG B 267
4	AC4	SOFTWARE	GLN B:138 , NAG B:267 , BMA B:269	BINDING SITE FOR RESIDUE NAG B 268
5	AC5	SOFTWARE	NAG B:268	BINDING SITE FOR RESIDUE BMA B 269
6	AC6	SOFTWARE	LEU A:76 , TYR A:77 , LEU A:78 , PHE A:90 , GLY A:114 , TYR A:116 , ILE A:158 , PRO A:162 , GLU A:163 , ARG A:166 , GLU A:194 , TRP A:197	BINDING SITE FOR RESIDUE PT1 A 321

Asymmetric 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 1HWP)

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

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

(no "Exon" information available for 1HWP)

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:252
 aligned with Q9AVR2_SAMEB | Q9AVR2 from UniProtKB/TrEMBL  Length:564

    Alignment length:252
                                    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 IDYPSVSFNLAGAKSTTYRDFLKNLRDRVATGTYEVNGLPVLRRESEVQVKNRFVLVRLTNYNGDTVTSAVDVTNLYLVAFSANGNSYFFKDATELQKSNLFLGTTQHTLSFTGNYDNLETAAGTRRESIELGPNPLDGAITSLWYDGGVARSLLVLIQMVPEAARFRYIEQEVRRSLQQLTSFTPNALMLSMENNWSSMSLEVQLSGDNVSPFSGTVQLQNYDHTPRLVDNFEELYKITGIAILLFRCVAT 277
               SCOP domains d1hwpa_ A: Ebulin A-chain                                                                                                                                                                                                                                    SCOP domains
               CATH domains -1hwpA01 A:2-165 Ricin (A subunit), domain 1                                                                                                                         1hwpA02 A:166-252 Ricin (A Subunit), domain 2                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeee....hhhhhhhhhhhhhhhhh....ee..eeee.hhhhhhhhh.eeeeeee.....eeeeeee.....eeeee...eeee....hhhhhh......ee.......hhhhhhhhhh.hhhhh..hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh....eeeeeeeee.....eeeeeehhhhhhhhh...ee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1hwp A   1 IDYPSVSFNLAGAKSTTYRDFLKNLRDRVATGTYEVNGLPVLRRESEVQVKNRFVLVRLTNYNGDTVTSAVDVTNLYLVAFSANGNSYFFKDATELQKSNLFLGTTQHTLSFTGNYDNLETAAGTRRESIELGPNPLDGAITSLWYDGGVARSLLVLIQMVPEAARFRYIEQEVRRSLQQLTSFTPNALMLSMENNWSSMSLEVQLSGDNVSPFSGTVQLQNYDHTPRLVDNFEELYKITGIAILLFRCVAT 252
                                    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:263
 aligned with Q9AVR2_SAMEB | Q9AVR2 from UniProtKB/TrEMBL  Length:564

    Alignment length:263
                                   309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559   
         Q9AVR2_SAMEB   300 GETCAIPAPFTRRIVGRDGLCVDVRNGYDTDGTPIQLWPCGTQRNQQWTFYNDKTIRSMGKCMTANGLNSGSYIMITDCSTAAEDATKWEVLIDGSIINPSSGLVMTAPSGASRTTLLLENNIHAASQGWTVSNDVQPIATLIVGYNEMCLQANGENNNVWMEDCDVTSVQQQWALFDDRTIRVNNSRGLCVTSNGYVSKDLIVIRKCQGLATQRWFFNSDGSVVNLKSTRVMDVKESDVSLQEVIIFPATGNPNQQWRTQVP 562
               SCOP domains d1hwpb1 B:2-135 Plant cytotoxin B-chain (lectin)                                                                                      d1hwpb2 B:136-264 Plant cytotoxin B-chain (lectin)                                                                                SCOP domains
               CATH domains 1hwpB01 B:2-138  [code=2.80.10.50, no name defined]                                                                                      1hwpB02 B:139-263  [code=2.80.10.50, no name defined]                                                                        - CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeee....eeeee.hhh....eeeeeee...hhhhheee.....eee..eeee..........ee......hhhhhh.eee...eee.....eeee..........eeee...hhhhh.eee......eeeeehhhhheeee......eeee.....hhhh.eee.....eee................ee.............eee.....eee.....eeee.hhhhhhh.eeee....hhhhh.eee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1hwp B   2 GETCAIPAPFTRRIVGRDGLCVDVRNGYDTDGTPIQLWPCGTQRNQQWTFYNDKTIRSMGKCMTANGLNSGSYIMITDCSTAAEDATKWEVLIDGSIINPSSGLVMTAPSGASRTTLLLENNIHAASQGWTVSNDVQPIATLIVGYNEMCLQANGENNNVWMEDCDVTSVQQQWALFDDRTIRVNNSRGLCVTSNGYVSKDLIVIRKCQGLATQRWFFNSDGSVVNLKSTRVMDVKESDVSLQEVIIFPATGNPNQQWRTQVP 264
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261

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 "Pfam Domain" information available for 1HWP)

Asymmetric 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 Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1hwp)

Biological Units
	Complete Structure
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		Biological Unit 2	[ Jena3D ]

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	1hwp
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	3.2.2.22
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UniProtKB/TrEMBL
	Q9AVR2_SAMEB \| Q9AVR2	:	1hwm 1hwn 1hwo

1hwm	1HWM IS EBULIN, ORTHORHOMBIC CRYSTAL FORM, DISTORTED 2GAMMA GALACTOSIDE-BINDING DOMAIN
1hwn	1HWN IS EBULIN COMPLEXED WITH GALACTOSE, TRIGONAL CRYSTAL FORM
1hwo	1HWO IS EBULIN COMPLEXED WITH LACTOSE, TRIGONAL CRYSTAL FORM

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 6)

Sites (6, 6)

SS Bonds (5, 5)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (2, 3)

CATH Domains (3, 4)

Pfam Domains (0, 0)

Gene Ontology (6, 6)

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Related Entries Specified in the PDB File