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Biological Unit 1 (Jmol Viewer)

Title :   STRUCTURE OF AVM-W110K (W110K MUTANT OF AVIDIN)

Authors :   Y. Pazy, Y. Eisenberg-Domovich, O. H. Laitinen, M. S. Kulomaa, E. A. Bayer, M. Wilchek, O. Livnah

Date :   22 Jan 03 (Deposition) - 15 Jul 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Avidin, Streptavidin, Biotin, Monomer-Monomer Interaction, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Pazy, Y. Eisenberg-Domovich, O. H. Laitinen, M. S. Kulomaa, E. A. Bayer, M. Wilchek, O. Livnah
Dimer-Tetramer Transition Between Solution And Crystalline States Of Streptavidin And Avidin Mutants.
J. Bacteriol. V. 185 4050 2003
PubMed-ID: 12837778 | Reference-DOI: 10.1128/JB.185.14.4050-4056.2003
(for further references see the PDB file header)

Molecule 1 - AVIDIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Cell Line	:	JM109
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	AVD
	Mutation	:	YES
	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)

(no "Ligand,Modified Residues,Ions" information available for 1NQN)

(no "Site" information available for 1NQN)

Asymmetric Unit

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

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

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	A:2-123
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	A:2-123
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:2-3 B:203-203	2 1
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 (gaps)	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:122
                                    35        45        55        65        75        85        95       105       115       125       135       145  
           AVID_CHICK    26 RKCSLTGKWTNDLGSNMTIGAVNSRGEFTGTYITAVTATSNEIKESPLHGTQNTINKRTQPTFGFTVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVNDIGDDWKATRVGINIFTRL 147
               SCOP domains d1nqna_ A: Avidin                                                                                                          SCOP domains
               CATH domains 1nqnA00 A:2-123  [code=2.40.128.30,     no name defined]                                                                   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee.....eeee.......eeeeeeeee.----..eeeeeeeeee.........eeeeee.......eeeeeeeeee.....eeeeeeeeee....hhhhhhh.eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- 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.Exon 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)
                 1nqn A   2 RKCSLTGKWTNDLGSNMTIGAVNSRGEFTGTYTTAV----NEIKESPLHGTENTINKRTQPTFGFTVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVNDIGDDKKATRVGINIFTRL 123
                                    11        21        31     |   -|       51        61        71        81        91       101       111       121  
                                                              37   42

Chain B from PDB  Type:PROTEIN  Length:111
 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 d1nqnb_ B: Avidin                                                                                                         SCOP domains
               CATH domains 1nqnB00 B:203-323  [code=2.40.128         .30, no name defined]                                                           CATH domains
           Pfam domains (1) -Avidin-1nqnB01 B:204-322                                                                                               - Pfam domains (1)
           Pfam domains (2) -Avidin-1nqnB02 B:204-322                                                                                               - Pfam domains (2)
         Sec.struct. author .....eeee.....eeee.......eeeeeee.---------..eeeeeee.........eeeeee.......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: B:204-274 (gaps) UniProt: 28-98                         ---------------------------------------Exon 1.6a  Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------Exon 1.5  PDB: B:274-314 (gaps)          --------- Transcript 1 (2)
                 1nqn B 203 KCSLTGKWTNDLGSNMTIGAVNSRGEFTGTYTT---------KESPLHGTENTINKRTQPTFGFTVNWKFSESTTVFTGQCFID-NGKEVLKTMWLLRSSVNDIGDDKKATRVGINIFTRL 323
                                   212       222       232  |      -  |    252       262       272       282   | | 292       302       312       322 
                                                          235       245                                      286 |                                   
                                                                                                               288

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	d1nqna_	A:
1b	d1nqnb_	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	1nqnA00	A:2-123
1b	1nqnB00	B:203-323

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

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

Family: Avidin (113)

Gallus gallus (Chicken) (13)

1a	Avidin-1nqnB01	B:204-322
1b	Avidin-1nqnB02	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 1nqn)

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	1nqn
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Description

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Ligands, Modified Residues, Ions (0, 0)

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SS Bonds (2, 2)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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Exons (4, 8)

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