2EPF - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Biological Unit 5 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF ZINC-BOUND PSEUDECIN FROM PSEUDECHIS PORPHYRIACUS

Authors :   N. Suzuki, Y. Yamazaki, Z. Fujimoto, T. Morita, H. Mizuno

Date :   29 Mar 07 (Deposition) - 11 Mar 08 (Release) - 29 Sep 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)
Biol. Unit 5: A (1x),B (1x),C (1x),D (1x)

Keywords :   Crisp, Snake Venom, Cng Channel, Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. Suzuki, Y. Yamazaki, R. L. Brown, Z. Fujimoto, T. Morita, H. Mizuno
Structures Of Pseudechetoxin And Pseudecin, Two Snake-Venom Cysteine-Rich Secretory Proteins That Target Cyclic Nucleotide-Gated Ion Channels: Implications For Movement Of The C-Terminal Cysteine-Rich Domain
Acta Crystallogr. , Sect. D V. 64 1034 2008
PubMed-ID: 18931410 | Reference-DOI: 10.1107/S0907444908023512

Molecule 1 - PSEUDECIN
	Chains	:	A, B, C, D
	Organism Common	:	RED-BELLIED BLACK SNAKE
	Organism Scientific	:	PSEUDECHIS PORPHYRIACUS
	Organism Taxid	:	8671
	Synonym	:	CHANNEL BLOCKER
	Tissue	:	VENOM

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C
Biological Unit 4 (1x)	:				D
Biological Unit 5 (1x)	:	A (1x)	B (1x)	C (1x)	D (1x)

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 8)

No.	Name	Count	Type	Full Name
1	NA	3	Ligand/Ion	SODIUM ION
2	ZN	5	Ligand/Ion	ZINC ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	NA	-1	Ligand/Ion	SODIUM ION
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	NA	-1	Ligand/Ion	SODIUM ION
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	NA	-1	Ligand/Ion	SODIUM ION
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 4 (0, 0)

No.	Name	Count	Type	Full Name
1	NA	-1	Ligand/Ion	SODIUM ION
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 5 (0, 0)

No.	Name	Count	Type	Full Name
1	NA	-1	Ligand/Ion	SODIUM ION
2	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:51 , HIS A:106 , HOH D:309	BINDING SITE FOR RESIDUE ZN A 301
2	AC2	SOFTWARE	HIS B:51 , HIS B:106 , HOH B:303	BINDING SITE FOR RESIDUE ZN B 302
3	AC3	SOFTWARE	HOH B:304 , HIS C:51 , HIS C:106	BINDING SITE FOR RESIDUE ZN C 303
4	AC4	SOFTWARE	HIS D:51 , HIS D:106 , HOH D:310 , HOH D:328	BINDING SITE FOR RESIDUE ZN D 304
5	AC5	SOFTWARE	HIS A:206 , HOH A:307 , HOH A:308 , PHE C:204 , HIS C:206	BINDING SITE FOR RESIDUE ZN A 305
6	AC6	SOFTWARE	SER A:72 , GLN A:73 , SER A:127 , SER A:128 , HOH A:309 , HOH A:379	BINDING SITE FOR RESIDUE NA A 306
7	AC7	SOFTWARE	SER C:72 , GLN C:73 , SER C:127 , HOH C:308	BINDING SITE FOR RESIDUE NA C 307
8	AC8	SOFTWARE	SER D:72 , GLN D:73 , SER D:127 , HOH D:313	BINDING SITE FOR RESIDUE NA D 308

Asymmetric Unit

No.	Residues
1	A:47	-	A:125
2	A:64	-	A:137
3	A:120	-	A:134
4	A:156	-	A:163
5	A:159	-	A:168
6	A:172	-	A:205
7	A:181	-	A:199
8	A:190	-	A:203
9	B:47	-	B:125
10	B:64	-	B:137
11	B:120	-	B:134
12	B:156	-	B:163
13	B:159	-	B:168
14	B:172	-	B:205
15	B:181	-	B:199
16	B:190	-	B:203
17	C:47	-	C:125
18	C:64	-	C:137
19	C:120	-	C:134
20	C:156	-	C:163
21	C:159	-	C:168
22	C:172	-	C:205
23	C:181	-	C:199
24	C:190	-	C:203
25	D:47	-	D:125
26	D:64	-	D:137
27	D:120	-	D:134
28	D:156	-	D:163
29	D:159	-	D:168
30	D:172	-	D:205
31	D:181	-	D:199
32	D:190	-	D:203

Asymmetric Unit

No.	Residues
1	Lys A:21	-	Pro A:22
2	Lys A:98	-	Pro A:99
3	Cys A:137	-	Pro A:138
4	Lys B:21	-	Pro B:22
5	Lys B:98	-	Pro B:99
6	Cys B:137	-	Pro B:138
7	Lys C:21	-	Pro C:22
8	Lys C:98	-	Pro C:99
9	Cys C:137	-	Pro C:138
10	Lys D:21	-	Pro D:22
11	Lys D:98	-	Pro D:99
12	Cys D:137	-	Pro D:138

(no "SAP(SNP)/Variant" information available for 2EPF)

Asymmetric Unit (3, 12)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CRISP_1	PS01009	CRISP family signature 1.	CRVP_PSEPO	133-143	4	A:105-115 B:105-115 C:105-115 D:105-115
2	CRISP_2	PS01010	CRISP family signature 2.	CRVP_PSEPO	159-170	4	A:131-142 B:131-142 C:131-142 D:131-142
3	SHKT	PS51670	ShKT domain profile.	CRVP_PSEPO	200-233	4	A:172-205 B:172-205 C:172-205 D:172-205

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_PSEPO	133-143	1	A:105-115 - - -
2	CRISP_2	PS01010	CRISP family signature 2.	CRVP_PSEPO	159-170	1	A:131-142 - - -
3	SHKT	PS51670	ShKT domain profile.	CRVP_PSEPO	200-233	1	A:172-205 - - -

Biological Unit 2 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CRISP_1	PS01009	CRISP family signature 1.	CRVP_PSEPO	133-143	1	- B:105-115 - -
2	CRISP_2	PS01010	CRISP family signature 2.	CRVP_PSEPO	159-170	1	- B:131-142 - -
3	SHKT	PS51670	ShKT domain profile.	CRVP_PSEPO	200-233	1	- B:172-205 - -

Biological Unit 3 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CRISP_1	PS01009	CRISP family signature 1.	CRVP_PSEPO	133-143	1	- - C:105-115 -
2	CRISP_2	PS01010	CRISP family signature 2.	CRVP_PSEPO	159-170	1	- - C:131-142 -
3	SHKT	PS51670	ShKT domain profile.	CRVP_PSEPO	200-233	1	- - C:172-205 -

Biological Unit 4 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CRISP_1	PS01009	CRISP family signature 1.	CRVP_PSEPO	133-143	1	- - - D:105-115
2	CRISP_2	PS01010	CRISP family signature 2.	CRVP_PSEPO	159-170	1	- - - D:131-142
3	SHKT	PS51670	ShKT domain profile.	CRVP_PSEPO	200-233	1	- - - D:172-205

Biological Unit 5 (3, 12)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CRISP_1	PS01009	CRISP family signature 1.	CRVP_PSEPO	133-143	4	A:105-115 B:105-115 C:105-115 D:105-115
2	CRISP_2	PS01010	CRISP family signature 2.	CRVP_PSEPO	159-170	4	A:131-142 B:131-142 C:131-142 D:131-142
3	SHKT	PS51670	ShKT domain profile.	CRVP_PSEPO	200-233	4	A:172-205 B:172-205 C:172-205 D:172-205

(no "Exon" information available for 2EPF)

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:207
 aligned with CRVP_PSEPO | Q8AVA3 from UniProtKB/Swiss-Prot  Length:238

    Alignment length:207
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       
           CRVP_PSEPO    32 NYQKEIVDKHNALRRSVKPTARNMLQMKWNSHAAQNAKRWADRCTFAHSPPNTRTVGKLRCGENIFMSSQPFPWSGVVQAWYDEIKNFVYGIGAKPPGSVIGHYTQVVWYKSHLIGCASAKCSSSKYLYVCQYCPAGNIRGSIATPYKSGPPCADCPSACVNRLCTNPCNYNNDFSNCKSLAKKSKCQTEWIKKKCPASCFCHNKII 238
               SCOP domains d2epfa1 A:4-153 automated matches                                                                                                                     d2epfa2 A:154-210 automated matches                       SCOP domains
               CATH domains 2epfA01 A:4-169 Pathogenesis-related Protein p14a                                                                                                                     ----------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh...........eehhhhhhhhhhhhh.......hhhh.ee..ee.eeeeeee....hhhhhhhhhhhhhh.ee...ee......hhhhhhhh.....eeeeeeeeee..eeeeeeeee.........................ee..ee...........hhhhhhhhhh..hhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------CRISP_1    ---------------CRISP_2     -----------------------------SHKT  PDB: A:172-205              ----- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2epf A   4 NYQKEIVDKHNALRRSVKPTARNMLQMKWNSHAAQNAKRWADRCTFAHSPPNTRTVGKLRCGENIFMSSQPFPWSGVVQAWYDEIKNFVYGIGAKPPGSVIGHYTQVVWYKSHLIGCASAKCSSSKYLYVCQYCPAGNIRGSIATPYKSGPPCADCPSACVNRLCTNPCNYNNDFSNCKSLAKKSKCQTEWIKKKCPASCFCHNKII 210
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203

Chain B from PDB  Type:PROTEIN  Length:207
 aligned with CRVP_PSEPO | Q8AVA3 from UniProtKB/Swiss-Prot  Length:238

    Alignment length:207
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       
           CRVP_PSEPO    32 NYQKEIVDKHNALRRSVKPTARNMLQMKWNSHAAQNAKRWADRCTFAHSPPNTRTVGKLRCGENIFMSSQPFPWSGVVQAWYDEIKNFVYGIGAKPPGSVIGHYTQVVWYKSHLIGCASAKCSSSKYLYVCQYCPAGNIRGSIATPYKSGPPCADCPSACVNRLCTNPCNYNNDFSNCKSLAKKSKCQTEWIKKKCPASCFCHNKII 238
               SCOP domains d2epfb1 B:4-153 automated matches                                                                                                                     d2epfb2 B:154-210 automated matches                       SCOP domains
               CATH domains 2epfB01 B:4-169 Pathogenesis-related Protein p14a                                                                                                                     ----------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh...........eehhhhhhhhhhhhh.......hhhh.ee..ee.eeeeeee....hhhhhhhhhhhhhh.ee...ee......hhhhhhhh.....eeeeeeeeee..eeeeeeeee.........................ee..ee...........hhhhhhhhhh..hhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------CRISP_1    ---------------CRISP_2     -----------------------------SHKT  PDB: B:172-205              ----- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2epf B   4 NYQKEIVDKHNALRRSVKPTARNMLQMKWNSHAAQNAKRWADRCTFAHSPPNTRTVGKLRCGENIFMSSQPFPWSGVVQAWYDEIKNFVYGIGAKPPGSVIGHYTQVVWYKSHLIGCASAKCSSSKYLYVCQYCPAGNIRGSIATPYKSGPPCADCPSACVNRLCTNPCNYNNDFSNCKSLAKKSKCQTEWIKKKCPASCFCHNKII 210
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203

Chain C from PDB  Type:PROTEIN  Length:207
 aligned with CRVP_PSEPO | Q8AVA3 from UniProtKB/Swiss-Prot  Length:238

    Alignment length:207
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       
           CRVP_PSEPO    32 NYQKEIVDKHNALRRSVKPTARNMLQMKWNSHAAQNAKRWADRCTFAHSPPNTRTVGKLRCGENIFMSSQPFPWSGVVQAWYDEIKNFVYGIGAKPPGSVIGHYTQVVWYKSHLIGCASAKCSSSKYLYVCQYCPAGNIRGSIATPYKSGPPCADCPSACVNRLCTNPCNYNNDFSNCKSLAKKSKCQTEWIKKKCPASCFCHNKII 238
               SCOP domains d2epfc1 C:4-153 automated matches                                                                                                                     d2epfc2 C:154-210 automated matches                       SCOP domains
               CATH domains 2epfC01 C:4-169 Pathogenesis-related Protein p14a                                                                                                                     ----------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh............eehhhhhhhhhhhhh.......hhhh.ee..ee.eeeeeee....hhhhhhhhhhhhhh.ee...ee......hhhhhhhh.....eeeeeeeeee..eeeeeeeee.........................ee..ee...........hhhhhhhhhh..hhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------CRISP_1    ---------------CRISP_2     -----------------------------SHKT  PDB: C:172-205              ----- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2epf C   4 NYQKEIVDKHNALRRSVKPTARNMLQMKWNSHAAQNAKRWADRCTFAHSPPNTRTVGKLRCGENIFMSSQPFPWSGVVQAWYDEIKNFVYGIGAKPPGSVIGHYTQVVWYKSHLIGCASAKCSSSKYLYVCQYCPAGNIRGSIATPYKSGPPCADCPSACVNRLCTNPCNYNNDFSNCKSLAKKSKCQTEWIKKKCPASCFCHNKII 210
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203

Chain D from PDB  Type:PROTEIN  Length:207
 aligned with CRVP_PSEPO | Q8AVA3 from UniProtKB/Swiss-Prot  Length:238

    Alignment length:207
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       
           CRVP_PSEPO    32 NYQKEIVDKHNALRRSVKPTARNMLQMKWNSHAAQNAKRWADRCTFAHSPPNTRTVGKLRCGENIFMSSQPFPWSGVVQAWYDEIKNFVYGIGAKPPGSVIGHYTQVVWYKSHLIGCASAKCSSSKYLYVCQYCPAGNIRGSIATPYKSGPPCADCPSACVNRLCTNPCNYNNDFSNCKSLAKKSKCQTEWIKKKCPASCFCHNKII 238
               SCOP domains d2epfd1 D:4-153 automated matches                                                                                                                     d2epfd2 D:154-210 automated matches                       SCOP domains
               CATH domains 2epfD01 D:4-169 Pathogenesis-related Protein p14a                                                                                                                     ----------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh...........eehhhhhhhhhhhhh.......hhhh.ee..ee.eeeeeee....hhhhhhhhhhhhhh.ee...ee........hhhhhh.....eeeeeeeeee..eeeeeeeee.........................ee..ee...........hhhhhhhhhh..hhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------CRISP_1    ---------------CRISP_2     -----------------------------SHKT  PDB: D:172-205              ----- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2epf D   4 NYQKEIVDKHNALRRSVKPTARNMLQMKWNSHAAQNAKRWADRCTFAHSPPNTRTVGKLRCGENIFMSSQPFPWSGVVQAWYDEIKNFVYGIGAKPPGSVIGHYTQVVWYKSHLIGCASAKCSSSKYLYVCQYCPAGNIRGSIATPYKSGPPCADCPSACVNRLCTNPCNYNNDFSNCKSLAKKSKCQTEWIKKKCPASCFCHNKII 210
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203

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: automated matches (4)

Protein domain: automated matches (4)

Pseudechis porphyriacus [TaxId: 8671] (2)

1a	d2epfa1	A:4-153
1b	d2epfb1	B:4-153
1c	d2epfc1	C:4-153
1d	d2epfd1	D:4-153

Class: Small proteins (3458)

Fold: Crisp domain-like (13)

Superfamily: Crisp domain-like (13)

Family: automated matches (8)

Protein domain: automated matches (8)

Pseudechis porphyriacus [TaxId: 8671] (2)

2a	d2epfa2	A:154-210
2b	d2epfb2	B:154-210
2c	d2epfc2	C:154-210
2d	d2epfd2	D:154-210

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)

Red-bellied black snake (Pseudechis porphyriacus) (2)

1a	2epfA01	A:4-169
1b	2epfB01	B:4-169
1c	2epfC01	C:4-169
1d	2epfD01	D:4-169

(no "Pfam Domain" information available for 2EPF)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (CRVP_PSEPO | Q8AVA3)

molecular function
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
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.

Asymmetric Unit
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		Lys D:98 - Pro D:99	[ RasMol ]

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	CRVP_PSEPO \| Q8AVA3
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	CRVP_PSEPO \| Q8AVA3	:	2ddb

2dda	PSEUDECHETOXIN
2ddb	APO FORM OF PSEUDECIN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 8)

Sites (8, 8)

SS Bonds (32, 32)

Cis Peptide Bonds (12, 12)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (3, 12)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 8)

CATH Domains (1, 4)

Pfam Domains (0, 0)

Gene Ontology (2, 2)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File