1XX5 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF NATRIN FROM NAJA ATRA SNAKE VENOM

Authors :   J. Wang, B. Shen, X. H. Lou, M. Guo, M. K. Teng, L. W. Niu

Date :   04 Nov 04 (Deposition) - 14 Jun 05 (Release) - 03 Dec 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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

Keywords :   Natrin, Crisps, Naja Atra, Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Wang, B. Shen, M. Guo, X. H. Lou, Y. Duan, X. P. Cheng, M. K. Teng, L. W. Niu, Q. Liu, Q. Huang, Q. Hao
Blocking Effect And Crystal Structure Of Natrin Toxin, A Cysteine-Rich Secretory Protein From Naja Atra Venom That Targets The Bkca Channel
Biochemistry V. 44 10145 2005
PubMed-ID: 16042391 | Reference-DOI: 10.1021/BI050614M
(for further references see the PDB file header)

Molecule 1 - NATRIN 1
	Chains	:	A, B, C
	Organism Common	:	CHINESE COBRA
	Organism Scientific	:	NAJA ATRA
	Organism Taxid	:	8656
	Synonym	:	CYSTEINE-RICH VENOM PROTEIN 1, NA-CRVP1

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	EOH	2	Ligand/Ion	ETHANOL

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	EOH	1	Ligand/Ion	ETHANOL

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	EOH	1	Ligand/Ion	ETHANOL

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	EOH	-1	Ligand/Ion	ETHANOL

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:75 , HOH A:511	BINDING SITE FOR RESIDUE EOH A 501
2	AC2	SOFTWARE	HIS B:60	BINDING SITE FOR RESIDUE EOH B 502

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
9	B:56	-	B:134
10	B:73	-	B:148
11	B:129	-	B:145
12	B:167	-	B:174
13	B:170	-	B:179
14	B:183	-	B:216
15	B:192	-	B:210
16	B:201	-	B:214
17	C:56	-	C:134
18	C:73	-	C:148
19	C:129	-	C:145
20	C:167	-	C:174
21	C:170	-	C:179
22	C:183	-	C:216
23	C:192	-	C:210
24	C:201	-	C:214

Asymmetric Unit

No.	Residues
1	Ser A:30	-	Pro A:31
2	Asn A:107	-	Pro A:108
3	Cys A:148	-	Pro A:149
4	Ser B:30	-	Pro B:31
5	Asn B:107	-	Pro B:108
6	Cys B:148	-	Pro B:149
7	Ser C:30	-	Pro C:31
8	Asn C:107	-	Pro C:108
9	Cys C:148	-	Pro C:149

(no "SAP(SNP)/Variant" information available for 1XX5)

Asymmetric Unit (3, 9)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CRISP_1	PS01009	CRISP family signature 1.	CRVP1_NAJAT	132-142	3	A:114-124 B:114-124 C:114-124
2	CRISP_2	PS01010	CRISP family signature 2.	CRVP1_NAJAT	160-171	3	A:142-153 B:142-153 C:142-153
3	SHKT	PS51670	ShKT domain profile.	CRVP1_NAJAT	201-234	3	A:183-216 B:183-216 C: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.	CRVP1_NAJAT	132-142	1	A:114-124 - -
2	CRISP_2	PS01010	CRISP family signature 2.	CRVP1_NAJAT	160-171	1	A:142-153 - -
3	SHKT	PS51670	ShKT domain profile.	CRVP1_NAJAT	201-234	1	A:183-216 - -

Biological Unit 2 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CRISP_1	PS01009	CRISP family signature 1.	CRVP1_NAJAT	132-142	1	- B:114-124 -
2	CRISP_2	PS01010	CRISP family signature 2.	CRVP1_NAJAT	160-171	1	- B:142-153 -
3	SHKT	PS51670	ShKT domain profile.	CRVP1_NAJAT	201-234	1	- B:183-216 -

Biological Unit 3 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CRISP_1	PS01009	CRISP family signature 1.	CRVP1_NAJAT	132-142	1	- - C:114-124
2	CRISP_2	PS01010	CRISP family signature 2.	CRVP1_NAJAT	160-171	1	- - C:142-153
3	SHKT	PS51670	ShKT domain profile.	CRVP1_NAJAT	201-234	1	- - C:183-216

(no "Exon" information available for 1XX5)

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:216
 aligned with CRVP1_NAJAT | Q7T1K6 from UniProtKB/Swiss-Prot  Length:239

    Alignment length:216
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233      
          CRVP1_NAJAT    24 SESTRRKKKQKEIVDLHNSLRRRVSPTASNMLKMEWYPEAASNAERWANTCSLNHSPDNLRVLEGIQCGESIYMSSNARTWTEIIHLWHDEYKNFVYGVGANPPGSVTGHYTQIVWYQTYRAGCAVSYCPSSAWSYFYVCQYCPSGNFQGKTATPYKLGPPCGDCPSACDNGLCTNPCTIYNKLTNCDSLLKQSSCQDDWIKSNCPASCFCRNKII 239
               SCOP domains d1xx5a1 A:6-164 automated matches                                                                                                                              d1xx5a2 A:165-221 automated matches                       SCOP domains
               CATH domains 1xx5A01 A:6-180 Pathogenesis-related Protein p14a                                                                                                                              ----------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhh...........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
                 1xx5 A   6 SESTRRKKKQKEIVDLHNSLRRRVSPTASNMLKMEWYPEAASNAERWANTCSLNHSPDNLRVLEGIQCGESIYMSSNARTWTEIIHLWHDEYKNFVYGVGANPPGSVTGHYTQIVWYQTYRAGCAVSYCPSSAWSYFYVCQYCPSGNFQGKTATPYKLGPPCGDCPSACDNGLCTNPCTIYNKLTNCDSLLKQSSCQDDWIKSNCPASCFCRNKII 221
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215

Chain B from PDB  Type:PROTEIN  Length:216
 aligned with CRVP1_NAJAT | Q7T1K6 from UniProtKB/Swiss-Prot  Length:239

    Alignment length:216
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233      
          CRVP1_NAJAT    24 SESTRRKKKQKEIVDLHNSLRRRVSPTASNMLKMEWYPEAASNAERWANTCSLNHSPDNLRVLEGIQCGESIYMSSNARTWTEIIHLWHDEYKNFVYGVGANPPGSVTGHYTQIVWYQTYRAGCAVSYCPSSAWSYFYVCQYCPSGNFQGKTATPYKLGPPCGDCPSACDNGLCTNPCTIYNKLTNCDSLLKQSSCQDDWIKSNCPASCFCRNKII 239
               SCOP domains d1xx5b1 B:6-164 automated matches                                                                                                                              d1xx5b2 B:165-221 automated matches                       SCOP domains
               CATH domains 1xx5B01 B:6-180 Pathogenesis-related Protein p14a                                                                                                                              ----------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhh...........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: B:183-216              ----- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1xx5 B   6 SESTRRKKKQKEIVDLHNSLRRRVSPTASNMLKMEWYPEAASNAERWANTCSLNHSPDNLRVLEGIQCGESIYMSSNARTWTEIIHLWHDEYKNFVYGVGANPPGSVTGHYTQIVWYQTYRAGCAVSYCPSSAWSYFYVCQYCPSGNFQGKTATPYKLGPPCGDCPSACDNGLCTNPCTIYNKLTNCDSLLKQSSCQDDWIKSNCPASCFCRNKII 221
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215

Chain C from PDB  Type:PROTEIN  Length:212
 aligned with CRVP1_NAJAT | Q7T1K6 from UniProtKB/Swiss-Prot  Length:239

    Alignment length:212
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237  
          CRVP1_NAJAT    28 RRKKKQKEIVDLHNSLRRRVSPTASNMLKMEWYPEAASNAERWANTCSLNHSPDNLRVLEGIQCGESIYMSSNARTWTEIIHLWHDEYKNFVYGVGANPPGSVTGHYTQIVWYQTYRAGCAVSYCPSSAWSYFYVCQYCPSGNFQGKTATPYKLGPPCGDCPSACDNGLCTNPCTIYNKLTNCDSLLKQSSCQDDWIKSNCPASCFCRNKII 239
               SCOP domains d1xx5c1 C:10-164 automated matches                                                                                                                         d1xx5c2 C:165-221 automated matches                       SCOP domains
               CATH domains 1xx5C01 C:10-180 Pathogenesis-related Protein p14a                                                                                                                         ----------------------------------------- CATH domains
           Pfam domains (1) ---------CAP-1xx5C04 C:19-147                                                                                                             -------------------Crisp-1xx5C01 C:167-221                                 Pfam domains (1)
           Pfam domains (2) ---------CAP-1xx5C05 C:19-147                                                                                                             -------------------Crisp-1xx5C02 C:167-221                                 Pfam domains (2)
           Pfam domains (3) ---------CAP-1xx5C06 C:19-147                                                                                                             -------------------Crisp-1xx5C03 C:167-221                                 Pfam domains (3)
         Sec.struct. author .hhhhhhhhhhhhhhhhh............eehhhhhhhhhhhhh.......hhhh.ee..ee.eeeeeee....hhhhhhhhhhhhhh.ee...ee......hhhhhhhh.....eeeeeeee.......eeeeeeee..........................................hhhhhhhhh...hhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------CRISP_1    -----------------CRISP_2     -----------------------------SHKT  PDB: C:183-216              ----- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xx5 C  10 RRKKKQKEIVDLHNSLRRRVSPTASNMLKMEWYPEAASNAERWANTCSLNHSPDNLRVLEGIQCGESIYMSSNARTWTEIIHLWHDEYKNFVYGVGANPPGSVTGHYTQIVWYQTYRAGCAVSYCPSSAWSYFYVCQYCPSGNFQGKTATPYKLGPPCGDCPSACDNGLCTNPCTIYNKLTNCDSLLKQSSCQDDWIKSNCPASCFCRNKII 221
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219

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)

Chinese cobra (Naja atra) [TaxId: 8656] (4)

1a	d1xx5a1	A:6-164
1b	d1xx5b1	B:6-164
1c	d1xx5c1	C:10-164

Class: Small proteins (3458)

Fold: Crisp domain-like (13)

Superfamily: Crisp domain-like (13)

Family: automated matches (8)

Protein domain: automated matches (8)

Chinese cobra (Naja atra) [TaxId: 8656] (4)

2a	d1xx5a2	A:165-221
2b	d1xx5b2	B:165-221
2c	d1xx5c2	C: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)

Chinese cobra (Naja atra) (3)

1a	1xx5C01	C:10-180
1b	1xx5A01	A:6-180
1c	1xx5B01	B:6-180

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: ShK-like (4)

Family: Crisp (3)

Naja atra (Chinese cobra) (3)

1a	Crisp-1xx5C01	C:167-221
1b	Crisp-1xx5C02	C:167-221
1c	Crisp-1xx5C03	C:167-221

Clan: no clan defined [family: CAP] (7)

Family: CAP (7)

Naja atra (Chinese cobra) (3)

2a	CAP-1xx5C04	C:19-147
2b	CAP-1xx5C05	C:19-147
2c	CAP-1xx5C06	C:19-147

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (CRVP1_NAJAT | Q7T1K6)

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

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(no "Related Entries Specified in the PDB File" available for 1XX5)

Description

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Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (24, 24)

Cis Peptide Bonds (9, 9)

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