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Biol. Unit 1 - sites (Jmol Viewer)

Title :   AVIDIN-NORBIOITN COMPLEX

Authors :   Y. Pazy, T. Kulik, E. A. Bayer, M. Wilchek, O. Livnah

Date :   09 Apr 02 (Deposition) - 06 Nov 02 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   Avidin, Streptavidin, Biotin, High Affinity Systems, Ligand Exchange, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Pazy, T. Kulik, E. A. Bayer, M. Wilchek, O. Livnah
Ligand Exchange Between Proteins: Exchange Of Biotin And Biotin Derivatives Between Avidin And Streptavidin
J. Biol. Chem. V. 277 30892 2002
PubMed-ID: 12055191 | Reference-DOI: 10.1074/JBC.M202874200

Molecule 1 - AVIDIN
	Chains	:	A, B
	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 (2, 4)

No.	Name	Count	Type	Full Name
1	NDG	2	Ligand/Ion	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
2	SNR	2	Ligand/Ion	NORBIOTIN

Biological Unit 1 (2, 8)

No.	Name	Count	Type	Full Name
1	NDG	4	Ligand/Ion	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
2	SNR	4	Ligand/Ion	NORBIOTIN

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:15 , ASN A:17 , THR A:34 , LEU A:123 , HOH A:435 , ALA B:222	BINDING SITE FOR RESIDUE NDG A 151
2	AC2	SOFTWARE	GLY B:215 , ASN B:217 , THR B:234 , HOH B:499	BINDING SITE FOR RESIDUE NDG B 352
3	AC3	SOFTWARE	ASN A:12 , LEU A:14 , SER A:16 , TYR A:33 , THR A:35 , VAL A:37 , THR A:38 , ALA A:39 , TRP A:70 , PHE A:72 , THR A:77 , TRP A:97 , TRP A:110 , ASN A:118	BINDING SITE FOR RESIDUE SNR A 150
4	AC4	SOFTWARE	ASN B:212 , LEU B:214 , SER B:216 , TYR B:233 , THR B:235 , THR B:238 , ALA B:239 , THR B:240 , TRP B:270 , PHE B:272 , THR B:277 , TRP B:297 , TRP B:310 , ASN B:318	BINDING SITE FOR RESIDUE SNR B 350

Asymmetric Unit

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

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

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 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	AVIDIN_1	PS00577	Avidin-like domain signature.	AVID_CHICK	132-146	2	A:108-122 B:308-322

Biological Unit 1 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	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:203-203	1 1
1.4	ENSGALT00000003855	4	ENSGALE00000024240	Z:8501440-8501650	211	AVID_CHICK	28-98	71	2	A:4-74 B:204-274	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: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 d1ldoa_ A: Avidin                                                                                                         SCOP domains
               CATH domains 1ldoA00 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) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------AVIDIN_1       - PROSITE
           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)
                 1ldo A   3 KCSLTGKWTNDLGSNMTIGAVNSRGEFTGTYTTAVTATSNEIKESPLHGTENTINKRTQPTFGFTVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVNDIGDDWKATRVGINIFTRL 123
                                    12        22        32        42        52        62        72        82        92       102       112       122

Chain B 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 d1ldob_ B: Avidin                                                                                                         SCOP domains
               CATH domains 1ldoB00 B:203-323  [code=2.40.128.30, no name defined]                                                                    CATH domains
           Pfam domains (1) -Avidin-1ldoB01 B:204-322                                                                                               - Pfam domains (1)
           Pfam domains (2) -Avidin-1ldoB02 B:204-322                                                                                               - Pfam domains (2)
         Sec.struct. author .....eeeee....eeee.......eeeeeee............eeeeeee.hhhhh...eeeeeee......eeeeeeeeee.....eeeeeeeeee....hhhhhhh.eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------T----------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------AVIDIN_1       - PROSITE
           Transcript 1 (1) 1Exon 1.4  PDB: B:204-274 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)
                 1ldo B 203 KCSLTGKWTNDLGSNMTIGAVNSRGEFTGTYTTAVTATSNEIKESPLHGTENTINKRTQPTFGFTVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVNDIGDDWKATRVGINIFTRL 323
                                   212       222       232       242       252       262       272       282       292       302       312       322

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	d1ldoa_	A:
1b	d1ldob_	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	1ldoA00	A:3-123
1b	1ldoB00	B:203-323

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

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

Family: Avidin (113)

Gallus gallus (Chicken) (13)

1a	Avidin-1ldoB01	B:204-322
1b	Avidin-1ldoB02	B:204-322

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 1ldo)

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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1lcv	STREPTAVIDIN-NORBIOTIN COMPLEX
1lcw	STREPTAVIDIN-HOMOBIOTIN COMPLEX
1lcz	STREPTAVIDIN-BCAP COMPLEX
1ldq	AVIDIN-HOMOBIOTIN COMPLEX
1lel	AVIDIN BCAP COMPLEX

Description

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Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (2, 2)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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Exons (4, 8)

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