3D7W - JenaLib

Asymmetric Unit (14, 14)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:91 , ASN A:112 , ASP A:117	BINDING SITE FOR RESIDUE NAG A 500
02	AC2	SOFTWARE	PHE B:276 , ASN B:308 , HOH B:855	BINDING SITE FOR RESIDUE NAG B 600
03	AC3	SOFTWARE	TRP B:341 , ASN B:343 , TYR B:373 , LEU B:475 , HOH B:731 , HOH B:802	BINDING SITE FOR RESIDUE NAG B 602
04	AC4	SOFTWARE	PHE A:214 , ASN A:215 , PRO A:217 , ILE B:258 , ASN B:291 , LEU B:296 , ASN B:383 , HOH B:744	BINDING SITE FOR RESIDUE NAG B 603
05	AC5	SOFTWARE	ILE B:258 , ASN B:291 , LEU B:296 , HOH B:746	BINDING SITE FOR RESIDUE NAG B 604
06	AC6	SOFTWARE	TRP B:341	BINDING SITE FOR RESIDUE NAG B 605
07	AC7	SOFTWARE	GLU A:119 , HIS A:124 , ARG A:125 , ASP A:126	BINDING SITE FOR RESIDUE SO4 A 660
08	AC8	SOFTWARE	GLY A:31 , SER A:32 , PHE A:33 , ASP B:249	BINDING SITE FOR RESIDUE SO4 A 661
09	AC9	SOFTWARE	ARG A:234 , ASP A:235 , HOH A:665 , LEU B:380 , ARG B:388 , LEU B:423 , TYR B:424 , GLY B:425 , PRO B:508 , PRO B:510 , HOH B:872 , HOH B:875	BINDING SITE FOR RESIDUE ZEA B 701
10	BC1	SOFTWARE	ARG A:234 , ASP A:235 , HOH A:665 , ARG B:388 , LEU B:423 , TYR B:424 , GLY B:425 , PRO B:508 , PRO B:510 , HOH B:872 , HOH B:875	BINDING SITE FOR RESIDUE ZEZ B 702
11	BC2	SOFTWARE	PRO A:171 , TRP A:174 , ARG A:175 , GLN A:178 , HOH A:740 , TYR B:393 , ASP B:397	BINDING SITE FOR RESIDUE GOL A 648
12	BC3	SOFTWARE	LEU A:75 , TYR A:76 , GLY A:113 , ILE A:160 , SER A:164 , ARG A:168	BINDING SITE FOR RESIDUE GOL A 652
13	BC4	SOFTWARE	ASP A:133 , SER A:185 , PHE B:326 , THR B:330 , ALA B:331 , HOH B:710 , HOH B:853	BINDING SITE FOR RESIDUE GOL B 650
14	BC5	SOFTWARE	ASP B:270 , ASP B:273 , GLN B:283 , LYS B:288 , ASN B:294 , HOH B:796	BINDING SITE FOR RESIDUE GOL B 651

SS Bonds (4, 4)

Cis Peptide Bonds (5, 5)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (19, 19)

Asymmetric/Biological Unit (19, 19)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
01	UniProt	VAR_ML1_VISAL_001 *	E	48	D	ML1_VISAL	---	---	A	E	15	D
02	UniProt	VAR_ML1_VISAL_002 *	N	145	T	ML1_VISAL	---	---	A	N	112	T
03	UniProt	VAR_ML1_VISAL_003 *	P	149	T	ML1_VISAL	---	---	A	P	116	T
04	UniProt	VAR_ML1_VISAL_004 *	T	173	S	ML1_VISAL	---	---	A	T	140	S
05	UniProt	VAR_ML1_VISAL_005 *	F	177	Y	ML1_VISAL	---	---	A	F	144	Y
06	UniProt	VAR_ML1_VISAL_006 *	T	184	A	ML1_VISAL	---	---	A	T	151	A
07	UniProt	VAR_ML1_VISAL_007 *	Y	212	D	ML1_VISAL	---	---	A	Y	179	D
08	UniProt	VAR_ML1_VISAL_008 *	A	217	E	ML1_VISAL	---	---	A	A	184	E
09	UniProt	VAR_ML1_VISAL_009 *	V	223	M	ML1_VISAL	---	---	A	V	190	M
10	UniProt	VAR_ML1_VISAL_010 *	I	251	F	ML1_VISAL	---	---	A	I	218	F
11	UniProt	VAR_ML1_VISAL_011 *	T	264	S	ML1_VISAL	---	---	A	T	231	S
12	UniProt	VAR_ML1_VISAL_012 *	D	268	S	ML1_VISAL	---	---	A	D	235	S
13	UniProt	VAR_ML1_VISAL_013 *	N	319	S	ML1_VISAL	---	---	B	N	265	S
14	UniProt	VAR_ML1_VISAL_014 *	G	357	N	ML1_VISAL	---	---	B	G	303	N
15	UniProt	VAR_ML1_VISAL_015 *	G	458	Q	ML1_VISAL	---	---	B	G	404	Q
16	UniProt	VAR_ML1_VISAL_016 *	C	495	V	ML1_VISAL	---	---	B	N	441	V
17	UniProt	VAR_ML1_VISAL_017 *	G	524	Y	ML1_VISAL	---	---	B	G	470	Y
18	UniProt	VAR_ML1_VISAL_018 *	N	531	S	ML1_VISAL	---	---	B	N	477	S
19	UniProt	VAR_ML1_VISAL_019 *	N	531	T	ML1_VISAL	---	---	B	N	477	T
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

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:249
 aligned with ML1_VISAL | P81446 from UniProtKB/Swiss-Prot  Length:564

    Alignment length:249
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273         
            ML1_VISAL    34 YERLRLRVTHQTTGEEYFRFITLLRDYVSSGSFSNEIPLLRQSTIPVSDAQRFVLVELTNEGGDSITAAIDVTNLYVVAYQAGDQSYFLRDAPRGAETHLFTGTTRSSLPFNGSYPDLERYAGHRDQIPLGIDQLIQSVTALRFPGGSTRTQARSILILIQMISEAARFNPILWRARQYINSGASFLPDVYMLELETSWGQQSTQVQQSTDGVFNNPIRLAIPPGNFVTLTNVRDVIASLAIMLFVCGE 282
               SCOP domains d3d7wa_ A: automated matches                                                                                                                                                                                                                              SCOP domains
               CATH domains 3d7wA01 A:1-167 Ricin (A subunit), domain 1                                                                                                                            3d7wA02 A:168-249 Ricin (A Subunit), domain 2                                      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....hhhhhhhhhhhhhhhheeeeee..eeee............eeeeeee.....eeeeeee.....eeeeee..eeee......hhhhhh....eeee.....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh...eeeeeeeeee...eeeeeeehhhhh............ Sec.struct. author
                 SAPs(SNPs) --------------D------------------------------------------------------------------------------------------------T---T-----------------------S---Y------A---------------------------D----E-----M---------------------------F------------S---S-------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d7w A   1 YERLRLRTDQQTTGEEYFSFITLLRDYVSSGSFSNNIPLLRQSTVPVSEGQRFVLVELTNAGGDTITAAIDVTNLYVVAYEAGNQSYFLSDAPAGAETQDFSGTTSSSQPFNGSYPDLERYAGHRDQIPLGIDQLIQSVTALRFPGGQTKTQARSILILIQMISEAARFNPILWRARQYINSGASFLPDVYMLELETSWGQQSTQVQHSTDGVFNNPIALAIAPGVIVTLTNIRDVIASLAIMLFVCGE 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:262
 aligned with ML1_VISAL | P81446 from UniProtKB/Swiss-Prot  Length:564

    Alignment length:262
                                   312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562  
            ML1_VISAL   303 DVTCSASEPTVRIVGRNGMCVDVRDDDFHDGNQIQLWPSKSNNDPNQLWTIKRDGTIRSNGSCLTTYGYTAGVYVMIFDCNTAVREATLWEIWGNGTIINPRSNLVLAASSGIKGTTLTVQTLDYTLGQGWLAGNDTAPREVTIYGFRDLCMESNGGSVWVETCVISQQNQRWALYGDGSIRPKQNQDQCLTCGRDSVSTVINIVSCSAGSSGQRWVFTNEGAILNLKNGLAMDVAQANPKLRRIIIYPATGKPNQMWLPVP 564
               SCOP domains d3d7wb1 B:249-384 automated matches                                                                                                     d3d7wb2 B:385-510 automated matches                                                                                            SCOP domains
               CATH domains 3d7wB01 B:249-386  [code=2.80.10.50, no name defined]                                                                                     3d7wB02 B:387-510  [code=2.80.10.50, no name defined]                                                                        CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........ee.eehhhhheeee.hhh......eeee......hhhhheee.....eee..eeeee........eeee.....hhhhhh.ee.....eee....eeee..........eee....hhhhh.ee......eeeeeehhhhheeeee..eeeee.....hhh.eeee.....eee.....eeee..........eeee....hhhh.eee.....eee.....eeee.........eeee....hhhhh.eee. Sec.struct. author
             SAPs(SNPs) (1) ----------------S-------------------------------------N----------------------------------------------------------------------------------------------------Q------------------------------------V----------------------------Y------S--------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T--------------------------------- SAPs(SNPs) (2)
                    PROSITE ------RICIN_B_LECTIN  PDB: B:255-382 UniProt: 309-436                                                                                 ---RICIN_B_LECTIN  PDB: B:386-509 UniProt: 440-563                                                                             - PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d7w B 249 DVTCTASEPIVRIVGRNGMTVDVRDDDFHDGNQIQLWPSKSNNDPNQLWTIKKDGTIRSNGSCLTTYGYTAGVYVMIFDCNTAVREATIWQIWGNGTIINPRSNLVLAASSGIKGTTLTVQTLDYTLGQGWLAGNDTAPRETTIYGFRDLCMESAGGSVYVETCTAGQENQRWALYGDGSIRPKQLQSQCLTNGRDSISTVINIVSCSAGSSGQRWVFTNEGAILNLKNGLAMDVAQANPSLQRIIIYPATGNPNQMWLPVP 510
                                   258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508

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 '\|'

Classification and Annotation

SCOP Domains (2, 3)

CATH Domains (3, 4)

Pfam Domains (0, 0)

Gene Ontology (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (ML1_VISAL | P81446)

molecular function
	GO:0030246	carbohydrate binding	Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
	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.

Visualization

Interactive Views

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		GOL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NAG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		ZEA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		ZEZ	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ RasMol ]	+environment [ RasMol ]
		BC1	[ RasMol ]	+environment [ RasMol ]
		BC2	[ RasMol ]	+environment [ RasMol ]
		BC3	[ RasMol ]	+environment [ RasMol ]
		BC4	[ RasMol ]	+environment [ RasMol ]
		BC5	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Ala B:484 - Gln B:485	[ RasMol ]
		Ala B:486 - Asn B:487	[ RasMol ]
		Gln B:485 - Ala B:486	[ RasMol ]
		Gly A:248 - Glu A:249	[ RasMol ]
		Ser B:489 - Leu B:490	[ RasMol ]

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	3d7w
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	ML1_VISAL \| P81446
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	3.2.2.22
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 14)

Sites (14, 14)