2ERP - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF VASCULAR APOPTOSIS-INDUCING PROTEIN-1(INHIBITOR-BOUND FORM)

Authors :   S. Takeda, T. Igarashi, S. Araki

Date :   25 Oct 05 (Deposition) - 20 Jun 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.95

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

Keywords :   Metalloprotease, Disintegrin, Calcium-Binding, Adam, Svmp, Mdc Protein, Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Takeda, T. Igarashi, H. Mori, S. Araki
Crystal Structures Of Vap1 Reveal Adams' Mdc Domain Architecture And Its Unique C-Shaped Scaffold
Embo J. V. 25 2388 2006
PubMed-ID: 16688218 | Reference-DOI: 10.1038/SJ.EMBOJ.7601131
(for further references see the PDB file header)

Molecule 1 - VASCULAR APOPTOSIS-INDUCING PROTEIN 1
	Chains	:	A, B
	Fragment	:	RESIDUES 184-610
	Organism Common	:	WESTERN DIAMONDBACK RATTLESNAKE
	Organism Scientific	:	CROTALUS ATROX
	Organism Taxid	:	8730
	Secretion	:	VENOM
	Synonym	:	VAP-1

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 13)

No.	Name	Count	Type	Full Name
1	3CO	1	Ligand/Ion	COBALT (III) ION
2	CA	4	Ligand/Ion	CALCIUM ION
3	GM6	2	Ligand/Ion	3-(N-HYDROXYCARBOXAMIDO)-2-ISOBUTYLPROPANOYL-TRP-METHYLAMIDE
4	NAG	4	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
5	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (3, 7)

No.	Name	Count	Type	Full Name
1	3CO	1	Ligand/Ion	COBALT (III) ION
2	CA	-1	Ligand/Ion	CALCIUM ION
3	GM6	2	Ligand/Ion	3-(N-HYDROXYCARBOXAMIDO)-2-ISOBUTYLPROPANOYL-TRP-METHYLAMIDE
4	NAG	4	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
5	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (3, 4)

No.	Name	Count	Type	Full Name
1	3CO	1	Ligand/Ion	COBALT (III) ION
2	CA	-1	Ligand/Ion	CALCIUM ION
3	GM6	1	Ligand/Ion	3-(N-HYDROXYCARBOXAMIDO)-2-ISOBUTYLPROPANOYL-TRP-METHYLAMIDE
4	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
5	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (13, 13)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	NAG A:2 , ASN A:218 , THR A:220 , ALA A:221 , THR A:224 , ARG B:453	BINDING SITE FOR RESIDUE NAG A 1
02	AC2	SOFTWARE	NAG A:1 , GLN B:442 , ARG B:477	BINDING SITE FOR RESIDUE NAG A 2
03	AC3	SOFTWARE	NAG B:4 , ASN B:218 , ALA B:221 , GLN B:543	BINDING SITE FOR RESIDUE NAG B 3
04	AC4	SOFTWARE	NAG B:3	BINDING SITE FOR RESIDUE NAG B 4
05	AC5	SOFTWARE	HIS A:335 , HIS A:339 , HIS A:345 , GM6 A:1002	BINDING SITE FOR RESIDUE ZN A 700
06	AC6	SOFTWARE	VAL A:405 , ASN A:408 , PHE A:410 , GLU A:412 , GLU A:415 , ASP A:418	BINDING SITE FOR RESIDUE CA A 701
07	AC7	SOFTWARE	ASP A:469 , MET A:470 , ASP A:472 , ASP A:483 , ARG A:484	BINDING SITE FOR RESIDUE CA A 702
08	AC8	SOFTWARE	HIS A:238 , HIS A:243	BINDING SITE FOR RESIDUE 3CO A 703
09	AC9	SOFTWARE	HIS B:335 , HIS B:339 , HIS B:345 , GM6 B:1001	BINDING SITE FOR RESIDUE ZN B 700
10	BC1	SOFTWARE	VAL B:405 , ASN B:408 , PHE B:410 , GLU B:412 , GLU B:415 , ASP B:418	BINDING SITE FOR RESIDUE CA B 701
11	BC2	SOFTWARE	ASP B:469 , MET B:470 , ASP B:472 , ASP B:483 , ARG B:484	BINDING SITE FOR RESIDUE CA B 702
12	BC3	SOFTWARE	PRO B:299 , THR B:300 , ALA B:301 , GLY B:302 , ALA B:332 , HIS B:335 , GLU B:336 , HIS B:339 , HIS B:345 , ALA B:360 , GLY B:361 , LEU B:363 , ZN B:700	BINDING SITE FOR RESIDUE GM6 B 1001
13	BC4	SOFTWARE	PRO A:299 , THR A:300 , ALA A:301 , GLY A:302 , ALA A:332 , HIS A:335 , GLU A:336 , HIS A:339 , HIS A:345 , ALA A:360 , GLY A:361 , LEU A:363 , ZN A:700	BINDING SITE FOR RESIDUE GM6 A 1002

Asymmetric Unit

No.	Residues
1	A:310	-	A:390
2	A:350	-	A:374
3	A:352	-	A:357
4	A:365	-	B:365
5	A:406	-	A:435
6	A:417	-	A:430
7	A:419	-	A:425
8	A:429	-	A:452
9	A:443	-	A:449
10	A:448	-	A:474
11	A:461	-	A:481
12	A:468	-	A:499
13	A:492	-	A:504
14	A:511	-	A:561
15	A:526	-	A:572
16	A:539	-	A:549
17	A:556	-	A:598
18	A:592	-	A:603
19	B:310	-	B:390
20	B:350	-	B:374
21	B:352	-	B:357
22	B:406	-	B:435
23	B:417	-	B:430
24	B:419	-	B:425
25	B:429	-	B:452
26	B:443	-	B:449
27	B:448	-	B:474
28	B:461	-	B:481
29	B:468	-	B:499
30	B:492	-	B:504
31	B:511	-	B:561
32	B:526	-	B:572
33	B:539	-	B:549
34	B:556	-	B:598
35	B:592	-	B:603

(no "Cis Peptide Bond" information available for 2ERP)

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

Asymmetric Unit (4, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADAM_MEPRO	PS50215	ADAM type metalloprotease domain profile.	VM3V1_CROAT	199-395	2	A:199-395 B:199-395
2	ZINC_PROTEASE	PS00142	Neutral zinc metallopeptidases, zinc-binding region signature.	VM3V1_CROAT	332-341	2	A:332-341 B:332-341
3	DISINTEGRIN_2	PS50214	Disintegrin domain profile.	VM3V1_CROAT	403-488	2	A:403-488 B:403-488
4	DISINTEGRIN_1	PS00427	Disintegrins signature.	VM3V1_CROAT	443-462	2	A:443-462 B:443-462

Biological Unit 1 (4, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADAM_MEPRO	PS50215	ADAM type metalloprotease domain profile.	VM3V1_CROAT	199-395	2	A:199-395 B:199-395
2	ZINC_PROTEASE	PS00142	Neutral zinc metallopeptidases, zinc-binding region signature.	VM3V1_CROAT	332-341	2	A:332-341 B:332-341
3	DISINTEGRIN_2	PS50214	Disintegrin domain profile.	VM3V1_CROAT	403-488	2	A:403-488 B:403-488
4	DISINTEGRIN_1	PS00427	Disintegrins signature.	VM3V1_CROAT	443-462	2	A:443-462 B:443-462

Biological Unit 2 (4, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADAM_MEPRO	PS50215	ADAM type metalloprotease domain profile.	VM3V1_CROAT	199-395	2	A:199-395 B:199-395
2	ZINC_PROTEASE	PS00142	Neutral zinc metallopeptidases, zinc-binding region signature.	VM3V1_CROAT	332-341	2	A:332-341 B:332-341
3	DISINTEGRIN_2	PS50214	Disintegrin domain profile.	VM3V1_CROAT	403-488	2	A:403-488 B:403-488
4	DISINTEGRIN_1	PS00427	Disintegrins signature.	VM3V1_CROAT	443-462	2	A:443-462 B:443-462

(no "Exon" information available for 2ERP)

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:426
 aligned with VM3V1_CROAT | Q9DGB9 from UniProtKB/Swiss-Prot  Length:610

    Alignment length:426
                                   194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604      
          VM3V1_CROAT   185 SNLTPEQQRYLNAKKYVKLFLVADYIMYLKYGRNLTAVRTRMYDIVNVITPIYHRMNIHVALVGLEIWSNTDKIIVQSSADVTLDLFAKWRATDLLSRKSHDNAQLLTGINFNGPTAGLGYLGGICNTMYSAGIVQDHSKIHHLVAIAMAHEMGHNLGMDHDKDTCTCGTRPCVMAGALSCEASFLFSDCSQKDHREFLIKNMPQCILKKPLKTDVVSPAVCGNYFVEVGEECDCGSPRTCRDPCCDATTCKLRQGAQCAEGLCCDQCRFKGAGTECRAAKDECDMADVCTGRSAECTDRFQRNGQPCKNNNGYCYNGKCPIMADQCIALFGPGATVSQDACFQFNREGNHYGYCRKEQNTKIACEPQDVKCGRLYCFPNSPENKNPCNIYYSPNDEDKGMVLPGTKCADRKACSNGQCVDVTTPY 610
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhh.eeeeeeeeehhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeee...........hhhhhhhhhhhhhhhh........eeeeee.........eee...........eeeee....hhhhhhhhhhhhhhhhh..............................hhhhhhhhhhhhhhhhhhhhhh.......................................................ee..ee.....eee.........ee.................ee....ee.......hhhhhhhhhhh...ee.hhhhhhhhh........ee....ee....hhhhhh...ee.................................eee....eee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) --------------ADAM_MEPRO  PDB: A:199-395 UniProt: 199-395                                                                                                                                                          -------DISINTEGRIN_2  PDB: A:403-488 UniProt: 403-488                                        -------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------------------------ZINC_PROTE-----------------------------------------------------------------------------------------------------DISINTEGRIN_1       ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2erp A 185 SNLTPEQQRYLNAKKYVKLFLVADYIMYLKYGRNLTAVRTRMYDIVNVITPIYHRMNIHVALVGLEIWSNTDKIIVQSSADVTLDLFAKWRATDLLSRKSHDNAQLLTGINFNGPTAGLGYLGGICNTMYSAGIVQDHSKIHHLVAIAMAHEMGHNLGMDHDKDTCTCGTRPCVMAGALSCEASFLFSDCSQKDHREFLIKNMPQCILKKPLKTDVVSPAVCGNYFVEVGEECDCGSPRTCRDPCCDATTCKLRQGAQCAEGLCCDQCRFKGAGTECRAAKDECDMADVCTGRSAECTDRFQRNGQPCKNNNGYCYNGKCPIMADQCIALFGPGATVSQDACFQFNREGNHYGYCRKEQNTKIACEPQDVKCGRLYCFPNSPENKNPCNIYYSPNDEDKGMVLPGTKCADRKACSNGQCVDVTTPY 610
                                   194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604

Chain B from PDB  Type:PROTEIN  Length:426
 aligned with VM3V1_CROAT | Q9DGB9 from UniProtKB/Swiss-Prot  Length:610

    Alignment length:426
                                   194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604      
          VM3V1_CROAT   185 SNLTPEQQRYLNAKKYVKLFLVADYIMYLKYGRNLTAVRTRMYDIVNVITPIYHRMNIHVALVGLEIWSNTDKIIVQSSADVTLDLFAKWRATDLLSRKSHDNAQLLTGINFNGPTAGLGYLGGICNTMYSAGIVQDHSKIHHLVAIAMAHEMGHNLGMDHDKDTCTCGTRPCVMAGALSCEASFLFSDCSQKDHREFLIKNMPQCILKKPLKTDVVSPAVCGNYFVEVGEECDCGSPRTCRDPCCDATTCKLRQGAQCAEGLCCDQCRFKGAGTECRAAKDECDMADVCTGRSAECTDRFQRNGQPCKNNNGYCYNGKCPIMADQCIALFGPGATVSQDACFQFNREGNHYGYCRKEQNTKIACEPQDVKCGRLYCFPNSPENKNPCNIYYSPNDEDKGMVLPGTKCADRKACSNGQCVDVTTPY 610
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhh.eeeeeeeeehhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeee...........hhhhhhhhhhhhhhhhhhhh....eeeeee.........eee...........eeeee....hhhhhhhhhhhhhhhhh..............................hhhhhhhhhhhhhhhh.hhhhh.......................................................ee..ee.....eee......ee.ee..........ee.....ee....ee.......hhhhhhhhhh...eee.hhhhhhhhhhh...................hhhhh..eeee.........ee................eee..eee....eee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) --------------ADAM_MEPRO  PDB: B:199-395 UniProt: 199-395                                                                                                                                                          -------DISINTEGRIN_2  PDB: B:403-488 UniProt: 403-488                                        -------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------------------------ZINC_PROTE-----------------------------------------------------------------------------------------------------DISINTEGRIN_1       ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2erp B 185 SNLTPEQQRYLNAKKYVKLFLVADYIMYLKYGRNLTAVRTRMYDIVNVITPIYHRMNIHVALVGLEIWSNTDKIIVQSSADVTLDLFAKWRATDLLSRKSHDNAQLLTGINFNGPTAGLGYLGGICNTMYSAGIVQDHSKIHHLVAIAMAHEMGHNLGMDHDKDTCTCGTRPCVMAGALSCEASFLFSDCSQKDHREFLIKNMPQCILKKPLKTDVVSPAVCGNYFVEVGEECDCGSPRTCRDPCCDATTCKLRQGAQCAEGLCCDQCRFKGAGTECRAAKDECDMADVCTGRSAECTDRFQRNGQPCKNNNGYCYNGKCPIMADQCIALFGPGATVSQDACFQFNREGNHYGYCRKEQNTKIACEPQDVKCGRLYCFPNSPENKNPCNIYYSPNDEDKGMVLPGTKCADRKACSNGQCVDVTTPY 610
                                   194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604

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 '\|'

(no "SCOP Domain" information available for 2ERP)

(no "CATH Domain" information available for 2ERP)

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (VM3V1_CROAT | Q9DGB9)

molecular function
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0004222	metalloendopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
	GO:0008237	metallopeptidase activity	Catalysis of the hydrolysis of peptide bonds by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
	GO:0008233	peptidase activity	Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0006915	apoptotic process	A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
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
(no "Cis Peptide Bonds" information available for 2erp)

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	2erp
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	VM3V1_CROAT \| Q9DGB9
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UniProtKB/Swiss-Prot
	VM3V1_CROAT \| Q9DGB9	:	2ero 2erq

2ero	THE SAME PROTEIN(ORTHORHOMBIC CRYSTAL FORM)
2erq	THE SAME PROTEIN(TETRAGONAL CRYSTAL FORM)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 13)

Sites (13, 13)

SS Bonds (35, 35)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (4, 8)

Exons (0, 0)

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Gene Ontology (9, 9)

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