2A5C - JenaLib

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Title :   STRUCTURE OF AVIDIN IN COMPLEX WITH THE LIGAND 8-OXODEOXYADENOSINE

Authors :   R. Conners, E. Hooley, S. Thomas, R. L. Brady

Date :   30 Jun 05 (Deposition) - 23 May 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

Keywords :   Avidin, Damaged Dna, 8-Oxodeoxyadenosine, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Conners, E. Hooley, A. R. Clarke, S. Thomas, R. L. Brady
Recognition Of Oxidatively Modified Bases Within The Biotin-Binding Site Of Avidin.
J. Mol. Biol. V. 357 263 2006
PubMed-ID: 16413579 | Reference-DOI: 10.1016/J.JMB.2005.12.054

Molecule 1 - AVIDIN
	Chains	:	A, B
	Organism Common	:	CHICKEN
	Organism Scientific	:	GALLUS GALLUS
	Organism Taxid	:	9031
	Other Details	:	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	8DA	2	Ligand/Ion	8-OXODEOXYADENOSINE
2	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 1 (2, 8)

No.	Name	Count	Type	Full Name
1	8DA	4	Ligand/Ion	8-OXODEOXYADENOSINE
2	NAG	4	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:15 , ASN A:17 , THR A:34 , THR A:35 , ILE A:44 , ALA B:22	BINDING SITE FOR RESIDUE NAG A 302
2	AC2	SOFTWARE	GLY B:15 , ASN B:17 , THR B:34 , LEU B:123	BINDING SITE FOR RESIDUE NAG B 301
3	AC3	SOFTWARE	LEU A:14 , TYR A:33 , TRP A:70 , THR A:77 , TRP A:110 , ASN A:118 , HOH A:314 , HOH A:319	BINDING SITE FOR RESIDUE 8DA A 303
4	AC4	SOFTWARE	LEU B:14 , TYR B:33 , THR B:35 , ALA B:36 , TRP B:70 , PHE B:72 , THR B:77 , TRP B:97 , TRP B:110 , ASN B:118 , HOH B:307	BINDING SITE FOR RESIDUE 8DA B 201

Asymmetric Unit

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

Asymmetric Unit

No.	Residues
1	Thr A:35	-	Ala A:36
2	Thr A:40	-	Ser A:41
3	Asn A:88	-	Gly A:89
4	Ala B:36	-	Val B:37
5	Ala B:39	-	Thr B:40

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	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	T	34	T
	* ID not provided by source

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

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	AVIDIN_2	PS51326	Avidin-like domain profile.	AVID_CHICK	26-149	2	A:2-123 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, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	AVIDIN_2	PS51326	Avidin-like domain profile.	AVID_CHICK	26-149	4	A:2-123 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:1-3 B:1-3	3 3
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:123
 aligned with AVID_CHICK | P02701 from UniProtKB/Swiss-Prot  Length:152

    Alignment length:123
                                    34        44        54        64        74        84        94       104       114       124       134       144   
           AVID_CHICK    25 ARKCSLTGKWTNDLGSNMTIGAVNSRGEFTGTYITAVTATSNEIKESPLHGTQNTINKRTQPTFGFTVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVNDIGDDWKATRVGINIFTRL 147
               SCOP domains d2a5ca_ A: automated matches                                                                                                SCOP domains
               CATH domains 2a5cA00 A:1-123  [code=2.40.128.30, no name defined]                                                                        CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee....eeee.......eeeeeee............eeeeeee.........eeeeeee......eeeeeeeee.......eeeeeeeee....hhhhhhh.eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------T----------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -AVIDIN_2  PDB: A:2-123 UniProt: 26-149                                                                                     PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------AVIDIN_1       - PROSITE (2)
           Transcript 1 (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)
                 2a5c A   1 ARKCSLTGKWTNDLGSNMTIGAVNSRGEFTGTYTTAVTATSNEIKESPLHGTENTINKRTQPTFGFTVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVNDIGDDWKATRVGINIFTRL 123
                                    10        20        30        40        50        60        70        80        90       100       110       120

Chain B from PDB  Type:PROTEIN  Length:123
 aligned with AVID_CHICK | P02701 from UniProtKB/Swiss-Prot  Length:152

    Alignment length:123
                                    34        44        54        64        74        84        94       104       114       124       134       144   
           AVID_CHICK    25 ARKCSLTGKWTNDLGSNMTIGAVNSRGEFTGTYITAVTATSNEIKESPLHGTQNTINKRTQPTFGFTVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVNDIGDDWKATRVGINIFTRL 147
               SCOP domains d2a5cb_ B: automated matches                                                                                                SCOP domains
               CATH domains 2a5cB00 B:1-123  [code=2.40.128.30, no name defined]                                                                        CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee....eeee.......eeeeeeee.........eeeeeeeee.hhhhh...eeeeeee......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) 1.1Exon 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)
                 2a5c B   1 ARKCSLTGKWTNDLGSNMTIGAVNSRGEFTGTYTTAVTATSNEIKESPLHGTENTINKRTQPTFGFTVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVNDIGDDWKATRVGINIFTRL 123
                                    10        20        30        40        50        60        70        80        90       100       110       120

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	d2a5ca_	A:
1b	d2a5cb_	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	2a5cA00	A:1-123
1b	2a5cB00	B:1-123

(no "Pfam Domain" information available for 2A5C)

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
		Ala B:36 - Val B:37	[ RasMol ]
		Ala B:39 - Thr B:40	[ RasMol ]
		Asn A:88 - Gly A:89	[ RasMol ]
		Thr A:35 - Ala A:36	[ RasMol ]
		Thr A:40 - Ser A:41	[ RasMol ]

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	2a5c
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Description

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Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (2, 2)

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