1WVR - JenaLib

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Title :   CRYSTAL STRUCTURE OF A CRISP FAMILY CA-CHANNEL BLOCKER DERIVED FROM SNAKE VENOM

Authors :   Y. Shikamoto, K. Suto, Y. Yamazaki, T. Morita, H. Mizuno

Date :   24 Dec 04 (Deposition) - 05 Jul 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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

Keywords :   Cysteine-Rich Secretory Protein, Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Shikamoto, K. Suto, Y. Yamazaki, T. Morita, H. Mizuno
Crystal Structure Of A Crisp Family Ca2+ -Channel Blocker Derived From Snake Venom.
J. Mol. Biol. V. 350 735 2005
PubMed-ID: 15953617 | Reference-DOI: 10.1016/J.JMB.2005.05.020
(for further references see the PDB file header)

Molecule 1 - TRIFLIN
	Chains	:	A
	Organism Scientific	:	TRIMERESURUS FLAVOVIRIDIS
	Organism Taxid	:	88087
	Strain	:	TOKUNOSHIMA

		1
Asymmetric Unit	:	A
Biological Unit 1 (1x)	:	A
Biological Unit 2 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 9)

No.	Name	Count	Type	Full Name
1	CD	9	Ligand/Ion	CADMIUM ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	CD	-1	Ligand/Ion	CADMIUM ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	CD	-1	Ligand/Ion	CADMIUM ION

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:60 , HIS A:115 , HOH A:423 , HOH A:469 , HOH A:526	BINDING SITE FOR RESIDUE CD A 301
2	AC2	SOFTWARE	GLU A:40 , HOH A:465	BINDING SITE FOR RESIDUE CD A 302
3	AC3	SOFTWARE	ASP A:175 , HOH A:524	BINDING SITE FOR RESIDUE CD A 303
4	AC4	SOFTWARE	GLU A:13 , GLU A:44	BINDING SITE FOR RESIDUE CD A 304
5	AC5	SOFTWARE	GLU A:7 , GLU A:17 , HOH A:455	BINDING SITE FOR RESIDUE CD A 305
6	AC6	SOFTWARE	ASP A:173 , ASN A:218 , LYS A:219 , HOH A:435 , HOH A:518	BINDING SITE FOR RESIDUE CD A 306
7	AC7	SOFTWARE	HIS A:91 , HIS A:94 , HOH A:424 , HOH A:488	BINDING SITE FOR RESIDUE CD A 307
8	AC8	SOFTWARE	ASP A:193 , HOH A:437	BINDING SITE FOR RESIDUE CD A 308
9	AC9	SOFTWARE	ASN A:1 , ASP A:5 , GLU A:188	BINDING SITE FOR RESIDUE CD A 309

Asymmetric Unit

No.	Residues
1	A:56	-	A:134
2	A:73	-	A:148
3	A:129	-	A:145
4	A:167	-	A:174
5	A:170	-	A:179
6	A:183	-	A:216
7	A:192	-	A:210
8	A:201	-	A:214

Asymmetric Unit

No.	Residues
1	Asn A:30	-	Pro A:31
2	Val A:107	-	Pro A:108
3	Cys A:148	-	Pro A:149

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

Asymmetric Unit (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CRISP_1	PS01009	CRISP family signature 1.	CRVP_PROFL	133-143	1	A:114-124
2	CRISP_2	PS01010	CRISP family signature 2.	CRVP_PROFL	161-172	1	A:142-153
3	SHKT	PS51670	ShKT domain profile.	CRVP_PROFL	202-235	1	A:183-216

Biological Unit 1 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CRISP_1	PS01009	CRISP family signature 1.	CRVP_PROFL	133-143	1	A:114-124
2	CRISP_2	PS01010	CRISP family signature 2.	CRVP_PROFL	161-172	1	A:142-153
3	SHKT	PS51670	ShKT domain profile.	CRVP_PROFL	202-235	1	A:183-216

Biological Unit 2 (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CRISP_1	PS01009	CRISP family signature 1.	CRVP_PROFL	133-143	2	A:114-124
2	CRISP_2	PS01010	CRISP family signature 2.	CRVP_PROFL	161-172	2	A:142-153
3	SHKT	PS51670	ShKT domain profile.	CRVP_PROFL	202-235	2	A:183-216

(no "Exon" information available for 1WVR)

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:221
 aligned with CRVP_PROFL | Q8JI39 from UniProtKB/Swiss-Prot  Length:240

    Alignment length:221
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239 
           CRVP_PROFL    20 NVDFDSESPRKPEIQNEIIDLHNSLRRSVNPTASNMLKMEWYPEAAANAERWAYRCIESHSSRDSRVIGGIKCGENIYMATYPAKWTDIIHAWHGEYKDFKYGVGAVPSDAVIGHYTQIVWYKSYRAGCAAAYCPSSKYSYFYVCQYCPAGNIIGKTATPYKSGPPCGDCPSDCDNGLCTNPCTRENEFTNCDSLVQKSSCQDNYMKSKCPASCFCQNKII 240
               SCOP domains d1wvra1 A:1-164 automated matches                                                                                                                                   d1wvra2 A:165-221 automated matches                       SCOP domains
               CATH domains 1wvrA01 A:1-180 Pathogenesis-related Protein p14a                                                                                                                                   ----------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhh...hhhhhhhhhhhhhhhhh............eehhhhhhhhhhhhh.......hhhh.ee..ee.eeeeeee....hhhhhhhhhhhhhh.ee...ee......hhhhhhhh.....eeeeeeee.......eeeeeeee.........................ee..ee...........hhhhhhhhh...hhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------CRISP_1    -----------------CRISP_2     -----------------------------SHKT  PDB: A:183-216              ----- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wvr A   1 NVDFDSESPRKPEIQNEIIDLHNSLRRSVNPTASNMLKMEWYPEAAANAERWAYRCIESHSSRDSRVIGGIKCGENIYMATYPAKWTDIIHAWHGEYKDFKYGVGAVPSDAVIGHYTQIVWYKSYRAGCAAAYCPSSKYSYFYVCQYCPAGNIIGKTATPYKSGPPCGDCPSDCDNGLCTNPCTRENEFTNCDSLVQKSSCQDNYMKSKCPASCFCQNKII 221
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220

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 Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: PR-1-like (14)

Superfamily: PR-1-like (14)

Family: PR-1-like (10)

Protein domain: automated matches (6)

Habu snake (Trimeresurus flavoviridis) [TaxId: 88087] (1)

d1wvra1

A:1-164

Class: Small proteins (3458)

Fold: Crisp domain-like (13)

Superfamily: Crisp domain-like (13)

Family: automated matches (8)

Protein domain: automated matches (8)

Habu snake (Trimeresurus flavoviridis) [TaxId: 88087] (1)

d1wvra2

A:165-221

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Pathogenesis-related Protein p14a (12)

Homologous Superfamily: Pathogenesis-related Protein p14a (12)

Trimeresurus flavoviridis. Organism_taxid: 88087. Strain: tokunoshima (1)

1wvrA01

A:1-180

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

Asymmetric Unit(hide GO term definitions)

Chain A (CRVP_PROFL | Q8JI39)

cellular component
	GO:0005576		extracellular region		The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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	Cis Peptide Bonds
		Asn A:30 - Pro A:31	[ RasMol ]
		Cys A:148 - Pro A:149	[ RasMol ]
		Val A:107 - Pro A:108	[ RasMol ]

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	1wvr
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Description

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Ligands, Modified Residues, Ions (1, 9)

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SS Bonds (8, 8)

Cis Peptide Bonds (3, 3)

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