3VCK - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   THAUMATIN BY LB HANGING DROP VAPOUR DIFFUSION AFTER 9.05 MGY X-RAY DOSE AT ESRF ID29 BEAMLINE (WORST CASE)

Authors :   L. Belmonte, E. Pechkova, D. Scudieri, C. Nicolini

Date :   04 Jan 12 (Deposition) - 21 Nov 12 (Release) - 21 Nov 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym./Biol. Unit : A

Keywords :   Radiation Damage, Thin Film, Langmuir-Blodgett, Lb, Plant Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Belmonte, E. Pechkova, S. Tripathi, D. Scudieri, C. Nicolini
Langmuir-Blodgett Nanotemplate And Radiation Resistance In Protein Crystals: State Of The Art.
Crit Rev Eukaryot Gene Expr V. 22 219 2012
PubMed-ID: 23140163 | Reference-DOI: 10.1615/CRITREVEUKARGENEEXPR.V22.I3.50

Molecule 1 - THAUMATIN I
	Chains	:	A
	Organism Common	:	KATEMFE
	Organism Scientific	:	THAUMATOCOCCUS DANIELLII
	Organism Taxid	:	4621

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 4)

No.	Name	Count	Type	Full Name
1	GOL	4	Ligand/Ion	GLYCEROL

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:89 , VAL A:184 , GOL A:304	BINDING SITE FOR RESIDUE GOL A 301
2	AC2	SOFTWARE	ILE A:105 , ASP A:147 , ALA A:148 , CYS A:149 , TYR A:157 , SER A:182 , HOH A:462	BINDING SITE FOR RESIDUE GOL A 302
3	AC3	SOFTWARE	THR A:54	BINDING SITE FOR RESIDUE GOL A 303
4	AC4	SOFTWARE	GLY A:47 , SER A:91 , TYR A:99 , ASP A:101 , THR A:190 , GOL A:301 , HOH A:427	BINDING SITE FOR RESIDUE GOL A 304

Asymmetric/Biological Unit

No.	Residues
1	A:9	-	A:204
2	A:56	-	A:66
3	A:71	-	A:77
4	A:121	-	A:193
5	A:126	-	A:177
6	A:134	-	A:145
7	A:149	-	A:158
8	A:159	-	A:164

Asymmetric/Biological Unit

No.	Residues
1	Pro A:83	-	Pro A:84

(no "SAP(SNP)/Variant" information available for 3VCK)

Asymmetric/Biological Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THAUMATIN_2	PS51367	Thaumatin family profile.	THM1_THADA	1-207	1	A:1-207
2	THAUMATIN_1	PS00316	Thaumatin family signature.	THM1_THADA	62-77	1	A:62-77

(no "Exon" information available for 3VCK)

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:207
 aligned with Q8RVT0_THADA | Q8RVT0 from UniProtKB/TrEMBL  Length:207

    Alignment length:207
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       
         Q8RVT0_THADA     1 ATFEIVNRCSYTVWAAASKGDAALDAGGRQLNSGESWTINVEPGTNGGKIWARTDCYFDDSGSGICKTGDCGGLLRCKRFGRPPTTLAEFSLNQYGKDYIDISNIKGFNVPMDFSPTTRGCRGVRCAADIVGQCPAKLKAPGGGCNDACTVFQTSEYCCTTGKCGPTEYSRFFKRLCPDAFSYVLDKPTTVTCPGSSNYRVTFCPTA 207
               SCOP domains d3vcka_ A: Thaumatin                                                                                                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....eeeeee....eeeeeeeee....eeeee.......eeeeeeeeeee.....eeeee..................eeeeeeee..eeeeeee........eeeee.......eee..hhhhhhhhhhh.......hhhhhhhhhhhhh.......hhhhhhhhhhh.............eeee....eeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vck A   1 ATFEIVNRCSYTVWAAASKGDAALDAGGRQLNSGESWTINVEPGTNGGKIWARTDCYFDDSGSGICKTGDCGGLLRCKRFGRPPTTLAEFSLNQYGKDYIDISNIKGFNVPMDFSPTTRGCRGVRCAADIVGQCPAKLKAPGGGCNDACTVFQTSEYCCTTGKCGPTEYSRFFKRLCPDAFSYVLDKPTTVTCPGSSNYRVTFCPTA 207
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200

Chain A from PDB  Type:PROTEIN  Length:207
 aligned with THM1_THADA | P02883 from UniProtKB/Swiss-Prot  Length:207

    Alignment length:207
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       
           THM1_THADA     1 ATFEIVNRCSYTVWAAASKGDAALDAGGRQLNSGESWTINVEPGTNGGKIWARTDCYFDDSGSGICKTGDCGGLLRCKRFGRPPTTLAEFSLNQYGKDYIDISNIKGFNVPMNFSPTTRGCRGVRCAADIVGQCPAKLKAPGGGCNDACTVFQTSEYCCTTGKCGPTEYSRFFKRLCPDAFSYVLDKPTTVTCPGSSNYRVTFCPTA 207
               SCOP domains d3vcka_ A: Thaumatin                                                                                                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....eeeeee....eeeeeeeee....eeeee.......eeeeeeeeeee.....eeeee..................eeeeeeee..eeeeeee........eeeee.......eee..hhhhhhhhhhh.......hhhhhhhhhhhhh.......hhhhhhhhhhh.............eeee....eeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) THAUMATIN_2  PDB: A:1-207 UniProt: 1-207                                                                                                                                                                        PROSITE (1)
                PROSITE (2) -------------------------------------------------------------THAUMATIN_1     ---------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vck A   1 ATFEIVNRCSYTVWAAASKGDAALDAGGRQLNSGESWTINVEPGTNGGKIWARTDCYFDDSGSGICKTGDCGGLLRCKRFGRPPTTLAEFSLNQYGKDYIDISNIKGFNVPMDFSPTTRGCRGVRCAADIVGQCPAKLKAPGGGCNDACTVFQTSEYCCTTGKCGPTEYSRFFKRLCPDAFSYVLDKPTTVTCPGSSNYRVTFCPTA 207
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200

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: Osmotin, thaumatin-like protein (82)

Superfamily: Osmotin, thaumatin-like protein (82)

Family: Osmotin, thaumatin-like protein (80)

Protein domain: Thaumatin (47)

Ketemfe (Thaumatococcus daniellii) [TaxId: 4621] (47)

d3vcka_

(no "CATH Domain" information available for 3VCK)

(no "Pfam Domain" information available for 3VCK)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (Q8RVT0_THADA | Q8RVT0)

Chain A (THM1_THADA | P02883)

cellular component
	GO:0031410		cytoplasmic vesicle		A vesicle found in the cytoplasm of a cell.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Pro A:83 - Pro A:84	[ RasMol ]

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	3vck
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	THM1_THADA \| P02883
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 4)

Sites (4, 4)

SS Bonds (8, 8)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 2)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 1)

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Pfam Domains (0, 0)

Gene Ontology (1, 1)

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