1IJ8 - JenaLib

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Title :   CRYSTAL STRUCTURE OF LITE AVIDIN-BNI COMPLEX

Authors :   O. Livnah, T. Huberman

Date :   25 Apr 01 (Deposition) - 12 Sep 01 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Avidin, Streptavidin, Pseudo Enzymatic Activity, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Huberman, Y. Eisenberg-Domovich, G. Gitlin, T. Kulik, E. A. Bayer, M. Wilchek, O. Livnah
Chicken Avidin Exhibits Pseudo-Catalytic Properties. Biochemical, Structural, And Electrostatic Consequences.
J. Biol. Chem. V. 276 32031 2001
PubMed-ID: 11395489 | Reference-DOI: 10.1074/JBC.M102018200

Molecule 1 - AVIDIN
	Chains	:	A, B
	Organism Common	:	CHICKEN
	Organism Scientific	:	GALLUS GALLUS
	Organism Taxid	:	9031
	Tissue	:	EGG WHITE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	BNI	2	Ligand/Ion	5-(2-OXO-HEXAHYDRO-THIENO[3,4-D]IMIDAZOL-6-YL)-PENTANOIC ACID (4-NITRO-PHENYL)-AMIDE
2	NDG	2	Ligand/Ion	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE

Biological Unit 1 (2, 8)

No.	Name	Count	Type	Full Name
1	BNI	4	Ligand/Ion	5-(2-OXO-HEXAHYDRO-THIENO[3,4-D]IMIDAZOL-6-YL)-PENTANOIC ACID (4-NITRO-PHENYL)-AMIDE
2	NDG	4	Ligand/Ion	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:15 , ASN A:17 , THR A:34 , LEU A:123	BINDING SITE FOR RESIDUE NDG A 401
2	AC2	SOFTWARE	GLY B:215 , ASN B:217 , THR B:234 , LEU B:323	BINDING SITE FOR RESIDUE NDG B 402
3	AC3	SOFTWARE	SER A:16 , TYR A:33 , TRP A:70 , PHE A:72 , SER A:73 , SER A:75 , THR A:77 , TRP A:97 , TRP A:110 , LYS A:111 , ASN A:118	BINDING SITE FOR RESIDUE BNI A 501
4	AC4	SOFTWARE	ASN B:212 , SER B:216 , TYR B:233 , TRP B:270 , PHE B:272 , SER B:273 , SER B:275 , THR B:277 , TRP B:297 , TRP B:310 , LYS B:311 , ASN B:318	BINDING SITE FOR RESIDUE BNI B 502

Asymmetric Unit

No.	Residues
1	A:4	-	A:83
2	B:204	-	B:283

(no "Cis Peptide Bond" information available for 1IJ8)

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	T	34 234	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 A/B	T	34 234	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:202-323
2	AVIDIN_1	PS00577	Avidin-like domain signature.	AVID_CHICK	132-146	2	A:108-122 B:308-322

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:202-323
2	AVIDIN_1	PS00577	Avidin-like domain signature.	AVID_CHICK	132-146	4	A:108-122 B:308-322

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:202-203	1 2
1.4	ENSGALT00000003855	4	ENSGALE00000024240	Z:8501440-8501650	211	AVID_CHICK	28-98	71	2	A:4-74 (gaps) B:204-274 (gaps)	71 71
1.5	ENSGALT00000003855	5	ENSGALE00000024243	Z:8502076-8502196	121	AVID_CHICK	98-138	41	2	A:74-114 B:274-314	41 41
1.6a	ENSGALT00000003855	6a	ENSGALE00000024241	Z:8502284-8502409	126	AVID_CHICK	138-152	15	2	A:114-123 B:314-323	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:118
 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 d1ij8a_ A: Avidin                                                                                                         SCOP domains
               CATH domains 1ij8A00 A:3-123  [code=2.40.128.30,    no name defined]                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee....eeee.......eeeeeeeee..---..eeeeeeeeee.hhhhh...eeeeeee......eeeeeeeeee.....eeeeeeeeee....hhhhhhh.eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- 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 (gaps) 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)
                 1ij8 A   3 KCSLTGKWTNDLGSNMTIGAVNSRGEFTGTYTTAVT---NEIKESPLHGTENTINKRTQPTFGFTVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVNDIGDDWKATRVGINIFTRL 123
                                    12        22        32     |  42        52        62        72        82        92       102       112       122 
                                                              38  42

Chain B from PDB  Type:PROTEIN  Length:119
 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 d1ij8b_ B: Avidin                                                                                                          SCOP domains
               CATH domains 1ij8B00 B:202-323  [code=2.40.128.30,    no name defined]                                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee....eeee.......eeeeeeeee..---..eeeeeeeeee.hhhhh...eeeeeee......eeeeeeeeee.....eeeeeeeeee....hhhhhhh.eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------T----------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) AVIDIN_2  PDB: B:202-323 UniProt: 26-149                                                                                   PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------------------AVIDIN_1       - PROSITE (2)
           Transcript 1 (1) 1.Exon 1.4  PDB: B:204-274 (gaps) UniProt: 28-98                         ---------------------------------------Exon 1.6a  Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------Exon 1.5  PDB: B:274-314 UniProt: 98-138 --------- Transcript 1 (2)
                 1ij8 B 202 RKCSLTGKWTNDLGSNMTIGAVNSRGEFTGTYTTAVT---NEIKESPLHGTENTINKRTQPTFGFTVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVNDIGDDWKATRVGINIFTRL 323
                                   211       221       231      |  -|      251       261       271       281       291       301       311       321  
                                                              238 242

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: Avidin (10)

Chicken (Gallus gallus) [TaxId: 9031] (10)

1a	d1ij8a_	A:
1b	d1ij8b_	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	1ij8B00	B:202-323
1b	1ij8A00	A:3-123

(no "Pfam Domain" information available for 1IJ8)

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.

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Biological Unit
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		Biological Unit 1	[ Jena3D ]

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1i9h	1I9H CONTAINS STREPTAVIDIN-BNA COMPLEX
2avi	2AVI CONTAINS AVIDIN-BIOTIN COMPLEX

Description

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SS Bonds (2, 2)

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