1VYO - JenaLib

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Title :   CRYSTAL STRUCTURE OF AVIDIN

Authors :   T. T. Airenne, M. S. Johnson, T. A. Salminen

Date :   03 May 04 (Deposition) - 20 Jul 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.48

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

Keywords :   Glycoprotein, Glycoprotein, Biotin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Repo, T. A. Paldanius, V. P. Hytonen, T. K. Nyholm, K. K. Halling, J. Huuskonen, O. T. Pentikainen, K. Rissanen, J. P. Slotte, T. T. Airenne, T. A. Salminen, M. S. Kulomaa, M. S. Johnson
Binding Properties Of Haba-Type Azo Derivatives To Avidin And Avidin-Related Protein 4.
Chem. Biol. V. 13 1029 2006
PubMed-ID: 17052607 | Reference-DOI: 10.1016/J.CHEMBIOL.2006.08.006

Molecule 1 - AVIDIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Common	:	CHICKEN
	Organism Scientific	:	GALLUS GALLUS
	Organism Taxid	:	9031

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 6)

No.	Name	Count	Type	Full Name
1	GOL	6	Ligand/Ion	GLYCEROL

Biological Unit 1 (1, 12)

No.	Name	Count	Type	Full Name
1	GOL	12	Ligand/Ion	GLYCEROL

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TRP A:70 , THR A:77 , TRP A:97 , TRP A:110 , ASN A:118 , GOL A:502 , HOH A:2008	BINDING SITE FOR RESIDUE GOL A 501
2	AC2	SOFTWARE	VAL A:37 , THR A:38 , ALA A:39 , TRP A:70 , PHE A:72 , SER A:73 , SER A:75 , GOL A:501	BINDING SITE FOR RESIDUE GOL A 502
3	AC3	SOFTWARE	LEU A:14 , ASP A:109 , TRP A:110 , GLY A:116 , ILE A:117 , HOH A:2066 , HOH A:2067 , HOH A:2068 , LYS B:94	BINDING SITE FOR RESIDUE GOL A 503
4	AC4	SOFTWARE	ALA A:22 , ASN A:24 , GLU A:28 , THR A:30 , HOH B:2053	BINDING SITE FOR RESIDUE GOL A 504
5	AC5	SOFTWARE	TRP B:70 , THR B:77 , TRP B:97 , ASN B:118 , GOL B:502 , HOH B:2080	BINDING SITE FOR RESIDUE GOL B 501
6	AC6	SOFTWARE	VAL B:37 , THR B:38 , ALA B:39 , TRP B:70 , SER B:73 , SER B:75 , LEU B:99 , GOL B:501	BINDING SITE FOR RESIDUE GOL B 502

Asymmetric Unit

No.	Residues
1	A:4	-	A:83
2	B:4	-	B:83

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

Asymmetric Unit (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_AVID_CHICK_001 *	I	58	T	AVID_CHICK	---	---	A/B	I	34	T
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (1, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_AVID_CHICK_001 *	I	58	T	AVID_CHICK	---	---	A/B	I	34	T
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric Unit (2, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	AVIDIN_2	PS51326	Avidin-like domain profile.	AVID_CHICK	26-149	1	B:2-123
2	AVIDIN_1	PS00577	Avidin-like domain signature.	AVID_CHICK	132-146	2	A:108-122 B:108-122

Biological Unit 1 (2, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	AVIDIN_2	PS51326	Avidin-like domain profile.	AVID_CHICK	26-149	2	B:2-123
2	AVIDIN_1	PS00577	Avidin-like domain signature.	AVID_CHICK	132-146	4	A:108-122 B:108-122

Asymmetric Unit (4, 8)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENSGALT00000003855	1	ENSGALE00000024242	Z:8485802-8485882	81	AVID_CHICK	1-27	27	2	A:3-3 B:2-3	1 2
1.4	ENSGALT00000003855	4	ENSGALE00000024240	Z:8501440-8501650	211	AVID_CHICK	28-98	71	2	A:4-74 B:4-74	71 71
1.5	ENSGALT00000003855	5	ENSGALE00000024243	Z:8502076-8502196	121	AVID_CHICK	98-138	41	2	A:74-114 B:74-114	41 41
1.6a	ENSGALT00000003855	6a	ENSGALE00000024241	Z:8502284-8502409	126	AVID_CHICK	138-152	15	2	A:114-123 B:114-123	10 10

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:121
 aligned with AVID_CHICK | P02701 from UniProtKB/Swiss-Prot  Length:152

    Alignment length:121
                                    36        46        56        66        76        86        96       106       116       126       136       146 
           AVID_CHICK    27 KCSLTGKWTNDLGSNMTIGAVNSRGEFTGTYITAVTATSNEIKESPLHGTQNTINKRTQPTFGFTVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVNDIGDDWKATRVGINIFTRL 147
               SCOP domains d1vyoa_ A: automated matches                                                                                              SCOP domains
               CATH domains 1vyoA00 A:3-123  [code=2.40.128.30, no name defined]                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee....eeee.......eeeeeee............eeeeeee.hhhhh...eeeeeee......eeeeeeeeee.....eeeeeeeeee....hhhhhhh.eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------T----------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) AVIDIN_2  PDB: - UniProt: 26-149                                                                                          PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------AVIDIN_1       - PROSITE (2)
           Transcript 1 (1) 1Exon 1.4  PDB: A:4-74 UniProt: 28-98                                   ---------------------------------------Exon 1.6a  Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------Exon 1.5  PDB: A:74-114 UniProt: 98-138  --------- Transcript 1 (2)
                 1vyo A   3 KCSLTGKWTNDLGSNMTIGAVNSRGEFTGTYITAVTATSNEIKESPLHGTQNTINKRTQPTFGFTVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVNDIGDDWKATRVGINIFTRL 123
                                    12        22        32        42        52        62        72        82        92       102       112       122

Chain B from PDB  Type:PROTEIN  Length:122
 aligned with AVID_CHICK | P02701 from UniProtKB/Swiss-Prot  Length:152

    Alignment length:122
                                    35        45        55        65        75        85        95       105       115       125       135       145  
           AVID_CHICK    26 RKCSLTGKWTNDLGSNMTIGAVNSRGEFTGTYITAVTATSNEIKESPLHGTQNTINKRTQPTFGFTVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVNDIGDDWKATRVGINIFTRL 147
               SCOP domains d1vyob_ B: automated matches                                                                                               SCOP domains
               CATH domains 1vyoB00 B:2-123  [code=2.40.128.30, no name defined]                                                                       CATH domains
           Pfam domains (1) --Avidin-1vyoB01 B:4-122                                                                                                 - Pfam domains (1)
           Pfam domains (2) --Avidin-1vyoB02 B:4-122                                                                                                 - Pfam domains (2)
         Sec.struct. author ......eeeee....eeee.......eeeeeee............eeeeeee.hhhhh...eeeeee.......eeeeeeeeee.....eeeeeeeeee....hhhhhhh.eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------T----------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) AVIDIN_2  PDB: B:2-123 UniProt: 26-149                                                                                     PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------------------AVIDIN_1       - PROSITE (2)
           Transcript 1 (1) 1.Exon 1.4  PDB: B:4-74 UniProt: 28-98                                   ---------------------------------------Exon 1.6a  Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------Exon 1.5  PDB: B:74-114 UniProt: 98-138  --------- Transcript 1 (2)
                 1vyo B   2 RKCSLTGKWTNDLGSNMTIGAVNSRGEFTGTYITAVTATSNEIKESPLHGTQNTINKRTQPTFGFTVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVNDIGDDWKATRVGINIFTRL 123
                                    11        21        31        41        51        61        71        81        91       101       111       121

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: All beta proteins (24004)

Fold: Streptavidin-like (225)

Superfamily: Avidin/streptavidin (197)

Family: Avidin/streptavidin (181)

Protein domain: automated matches (50)

Chicken (Gallus gallus) [TaxId: 9031] (23)

1a	d1vyoa_	A:
1b	d1vyob_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: Lipocalin (526)

Homologous Superfamily: [code=2.40.128.30, no name defined] (148)

Chicken (Gallus gallus) (26)

1a	1vyoA00	A:3-123
1b	1vyoB00	B:2-123

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Avidin] (113)

Family: Avidin (113)

Gallus gallus (Chicken) (13)

1a	Avidin-1vyoB01	B:4-122
1b	Avidin-1vyoB02	B:4-122

Asymmetric Unit(hide GO term definitions)

Chain A,B (AVID_CHICK | P02701)

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 1vyo)

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	1vyo
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1avd	AVIDIN COMPLEX WITH BIOTIN
1ave	AVIDIN (APO FORM)
1ij8	CRYSTAL STRUCTURE OF LITE AVIDIN-BNI COMPLEX
1ldo	AVIDIN-NORBIOITN COMPLEX
1ldq	AVIDIN-HOMOBIOTIN COMPLEX
1lel	THE AVIDIN BCAP COMPLEX
1nqn	STRAYCTURE OF AVM-W110K (W110K MUTANT OF AVIDIN)
1rav	RECOMBINANT AVIDIN
2avi	AVIDIN COMPLEX WITH BIOTIN
2cam	AVIDIN MUTANT (K3E,K9E,R26D,R124L)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 6)

Sites (6, 6)

SS Bonds (2, 2)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 2)

PROSITE Motifs (2, 3)

Exons (4, 8)

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