1FVU - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF BOTROCETIN

Authors :   U. Sen, S. Vasudevan, G. Subbarao, R. A. Mcclintoc, R. Celikel, Z. M. Ruggeri, K. I. Varughese

Date :   20 Sep 00 (Deposition) - 14 Feb 01 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

Chains :   Asym./Biol. Unit : A,B,C,D

Keywords :   Von Willbrand Factor Modulator, C-Type Lectin, Metal- Binding, Loop Exchanged Dimer, Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   U. Sen, S. Vasudevan, G. Subbarao, R. A. Mcclintock, R. Celikel, Z. M. Ruggeri, K. I. Varughese
Crystal Structure Of The Von Willebrand Factor Modulator Botrocetin.
Biochemistry V. 40 345 2001
PubMed-ID: 11148028 | Reference-DOI: 10.1021/BI0021737
(for further references see the PDB file header)

Molecule 1 - BOTROCETIN ALPHA CHAIN
	Chains	:	A, C
	Organism Common	:	JARARACA
	Organism Scientific	:	BOTHROPS JARARACA
	Organism Taxid	:	8724
	Secretion	:	VENOM
	Synonym	:	PLATELET COAGGLUTININ ALPHA

Molecule 2 - BOTROCETIN BETA CHAIN
	Chains	:	B, D
	Organism Common	:	JARARACA
	Organism Scientific	:	BOTHROPS JARARACA
	Organism Taxid	:	8724
	Secretion	:	VENOM
	Synonym	:	PLATELET COAGGLUTININ BETA

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	MG	2	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER B:441 , GLU B:447 , GLU B:522	BINDING SITE FOR RESIDUE MG B 1001
2	AC2	SOFTWARE	SER D:641 , GLN D:643 , GLU D:647 , GLU D:722	BINDING SITE FOR RESIDUE MG D 1002

Asymmetric/Biological Unit

No.	Residues
1	A:2	-	A:13
2	A:30	-	A:128
3	A:80	-	B:475
4	A:103	-	A:120
5	B:402	-	B:413
6	B:430	-	B:521
7	B:498	-	B:513
8	C:202	-	C:213
9	C:230	-	C:328
10	C:280	-	D:675
11	C:303	-	C:320
12	D:602	-	D:613
13	D:630	-	D:721
14	D:698	-	D:713

(no "Cis Peptide Bond" information available for 1FVU)

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

Asymmetric/Biological Unit (2, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	C_TYPE_LECTIN_2	PS50041	C-type lectin domain profile.	SLEA_BOTJA	9-129	2	A:9-129 C:209-329
1	C_TYPE_LECTIN_2	PS50041	C-type lectin domain profile.	SLEB_BOTJA	9-122	2	B:409-522 D:609-722
2	C_TYPE_LECTIN_1	PS00615	C-type lectin domain signature.	SLEA_BOTJA	103-128	2	A:103-128 C:303-328

(no "Exon" information available for 1FVU)

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:133
 aligned with SLEA_BOTJA | P22029 from UniProtKB/Swiss-Prot  Length:133

    Alignment length:133
                                    10        20        30        40        50        60        70        80        90       100       110       120       130   
           SLEA_BOTJA     1 DCPSGWSSYEGNCYKFFQQKMNWADAERFCSEQAKGGHLVSIKIYSKEKDFVGDLVTKNIQSSDLYAWIGLRVENKEKQCSSEWSDGSSVSYENVVERTVKKCFALEKDLGFVLWINLYCAQKNPFVCKSPPP 133
               SCOP domains d1fvua_ A: Snake coagglutinin alpha chain                                                                                             SCOP domains
               CATH domains 1fvuA00 A:1-133 Mannose-Binding Protein A, subunit A                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee..eeeeeeeeeehhhhhhhhhhhhh...ee.......hhhhhhhhhhhhhh.....eeeeeeee......................hhhhh..eeeee.......eeee.....eeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------C_TYPE_LECTIN_2  PDB: A:9-129 UniProt: 9-129                                                                             ---- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) ------------------------------------------------------------------------------------------------------C_TYPE_LECTIN_1           ----- PROSITE (3)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1fvu A   1 DCPSGWSSYEGNCYKFFQQKMNWADAERFCSEQAKGGHLVSIKIYSKEKDFVGDLVTKNIQSSDLYAWIGLRVENKEKQCSSEWSDGSSVSYENVVERTVKKCFALEKDLGFVLWINLYCAQKNPFVCKSPPP 133
                                    10        20        30        40        50        60        70        80        90       100       110       120       130

Chain B from PDB  Type:PROTEIN  Length:121
 aligned with SLEB_BOTJA | P22030 from UniProtKB/Swiss-Prot  Length:125

    Alignment length:125
                                    10        20        30        40        50        60        70        80        90       100       110       120     
           SLEB_BOTJA     1 DCPPDWSSYEGHCYRFFKEWMHWDDAEEFCTEQQTGAHLVSFQSKEEADFVRSLTSEMLKGDVVWIGLSDVWNKCRFEWTDGMEFDYDDYYLIAEYECVASKPTNNKWWIIPCTRFKNFVCEFQA 125
               SCOP domains d1fvub_ B: Snake coagglutinin beta chain                                                                                      SCOP domains
               CATH domains 1fvuB00 B:401-525 Mannose-Binding Protein A, subunit A                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee..eeeeeeeeeehhhhhhhhhhhhh...ee....hhhhhhhhhh..........ee...........eee........----.....eeeeee....eeeeee....eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) --------C_TYPE_LECTIN_2  PDB: B:409-522 UniProt: 9-122                                                                    --- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 1fvu B 401 DCPPDWSSYEGHCYRFFKEWMHWDDAEEFCTEQQTGAHLVSFQSKEEADFVRSLTSEMLKGDVVWIGLSDVWNKCRFEWTDGMEFDY----LIAEYECVASKPTNNKWWIIPCTRFKNFVCEFQA 525
                                   410       420       430       440       450       460       470       480      |  - |     500       510       520     
                                                                                                                487  492

Chain C from PDB  Type:PROTEIN  Length:133
 aligned with SLEA_BOTJA | P22029 from UniProtKB/Swiss-Prot  Length:133

    Alignment length:133
                                    10        20        30        40        50        60        70        80        90       100       110       120       130   
           SLEA_BOTJA     1 DCPSGWSSYEGNCYKFFQQKMNWADAERFCSEQAKGGHLVSIKIYSKEKDFVGDLVTKNIQSSDLYAWIGLRVENKEKQCSSEWSDGSSVSYENVVERTVKKCFALEKDLGFVLWINLYCAQKNPFVCKSPPP 133
               SCOP domains d1fvuc_ C: Snake coagglutinin alpha chain                                                                                             SCOP domains
               CATH domains 1fvuC00 C:201-333 Mannose-Binding Protein A, subunit A                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee..eeeeeeeeeehhhhhhhhhhhhh...ee.......hhhhhhhhhhhh.......eeeeeeee......................hhhhh..eeeee.......eeee.....eeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------C_TYPE_LECTIN_2  PDB: C:209-329 UniProt: 9-129                                                                           ---- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) ------------------------------------------------------------------------------------------------------C_TYPE_LECTIN_1           ----- PROSITE (3)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1fvu C 201 DCPSGWSSYEGNCYKFFQQKMNWADAERFCSEQAKGGHLVSIKIYSKEKDFVGDLVTKNIQSSDLYAWIGLRVENKEKQCSSEWSDGSSVSYENVVERTVKKCFALEKDLGFVLWINLYCAQKNPFVCKSPPP 333
                                   210       220       230       240       250       260       270       280       290       300       310       320       330

Chain D from PDB  Type:PROTEIN  Length:121
 aligned with SLEB_BOTJA | P22030 from UniProtKB/Swiss-Prot  Length:125

    Alignment length:125
                                    10        20        30        40        50        60        70        80        90       100       110       120     
           SLEB_BOTJA     1 DCPPDWSSYEGHCYRFFKEWMHWDDAEEFCTEQQTGAHLVSFQSKEEADFVRSLTSEMLKGDVVWIGLSDVWNKCRFEWTDGMEFDYDDYYLIAEYECVASKPTNNKWWIIPCTRFKNFVCEFQA 125
               SCOP domains d1fvud_ D: Snake coagglutinin beta chain                                                                                      SCOP domains
               CATH domains 1fvuD00 D:601-725 Mannose-Binding Protein A, subunit A                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee..eeeeeeeeeehhhhhhhhhhh.....ee....hhhhhhhhhh..........eeeeee.......eee........----.....eeeeee....eeeeee....eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) --------C_TYPE_LECTIN_2  PDB: D:609-722 UniProt: 9-122                                                                    --- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 1fvu D 601 DCPPDWSSYEGHCYRFFKEWMHWDDAEEFCTEQQTGAHLVSFQSKEEADFVRSLTSEMLKGDVVWIGLSDVWNKCRFEWTDGMEFDY----LIAEYECVASKPTNNKWWIIPCTRFKNFVCEFQA 725
                                   610       620       630       640       650       660       670       680      |  - |     700       710       720     
                                                                                                                687  692

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

Fold: C-type lectin-like (322)

Superfamily: C-type lectin-like (322)

Family: C-type lectin domain (182)

Protein domain: Snake coagglutinin alpha chain (23)

Jararaca (Bothrops jararaca), botrocetin [TaxId: 8724] (4)

1a	d1fvua_	A:
1b	d1fvuc_	C:

Protein domain: Snake coagglutinin beta chain (23)

Jararaca (Bothrops jararaca), botrocetin [TaxId: 8724] (4)

2a	d1fvub_	B:
2b	d1fvud_	D:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Roll (3276)

Topology: Mannose-Binding Protein A; Chain A (180)

Homologous Superfamily: Mannose-Binding Protein A, subunit A (180)

Jararaca (Bothrops jararaca) (2)

1a	1fvuA00	A:1-133
1b	1fvuC00	C:201-333
1c	1fvuB00	B:401-525
1d	1fvuD00	D:601-725

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,C (SLEA_BOTJA | P22029)

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.

Chain B,D (SLEB_BOTJA | P22030)

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/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1fvu)

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	1fvu
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	SLEB_BOTJA \| P22030
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	SLEA_BOTJA \| P22029
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UniProtKB/Swiss-Prot
	SLEA_BOTJA \| P22029	:	1ijk 1u0n 1u0o
	SLEB_BOTJA \| P22030	:	1ijk 1u0n 1u0o

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

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (14, 14)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 6)

Exons (0, 0)

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