2C4I - JenaLib

Biol.Unit 1 - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF ENGINEERED AVIDIN

Authors :   V. P. Hytonen, J. Horha, T. T. Airenne, E. A. Niskanen, K. Helttunen, M. S. Johnson, T. A. Salminen, M. S. Kulomaa, H. R. Nordlund

Date :   19 Oct 05 (Deposition) - 05 Jul 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.95

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

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

Reference :   V. P. Hytonen, J. Horha, T. T. Airenne, E. A. Niskanen, K. Helttunen, M. S. Johnson, T. A. Salminen, M. S. Kulomaa, H. R. Nordlund
Controlling Quaternary Structure Assembly: Subunit Interface Engineering And Crystal Structure Of Dual Chain Avidin.
J. Mol. Biol. V. 359 1352 2006
PubMed-ID: 16787776 | Reference-DOI: 10.1016/J.JMB.2006.04.044

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

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 3)

No.	Name	Count	Type	Full Name
1	BTN	2	Ligand/Ion	BIOTIN
2	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 6)

No.	Name	Count	Type	Full Name
1	BTN	4	Ligand/Ion	BIOTIN
2	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:155 , LYS A:156 , GLU A:157 , ARG A:188 , HOH A:2117 , HOH A:2118	BINDING SITE FOR RESIDUE SO4 A1276
2	AC2	SOFTWARE	TRP A:15 , PHE A:17 , SER A:18 , SER A:20 , THR A:22 , TRP A:42 , TRP A:55 , ASN A:63 , ASN A:91 , SER A:95 , TYR A:112 , THR A:114 , VAL A:116 , THR A:117 , ALA A:118 , THR A:119 , HOH A:2115	BINDING SITE FOR RESIDUE BTN A1274
3	AC3	SOFTWARE	SER A:141 , THR A:143 , TRP A:163 , TRP A:176 , ASN A:184 , ASN A:212 , LEU A:214 , SER A:216 , TYR A:233 , THR A:235 , VAL A:237 , THR A:238 , ALA A:239 , THR A:240 , TRP A:270 , SER A:273 , HOH A:2116	BINDING SITE FOR RESIDUE BTN A1275

Asymmetric Unit

No.	Residues
1	A:28	-	A:83
2	A:149	-	A:204

(no "Cis Peptide Bond" information available for 2C4I)

Asymmetric Unit (1, 1)

								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	I	113	T
	* ID not provided by source

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

Biological Unit 1 (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	I	113	T
	* ID not provided by source

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

Asymmetric Unit (2, 2)

	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:82-260
2	AVIDIN_1	PS00577	Avidin-like domain signature.	AVID_CHICK	132-146	1	A:174-188

Biological Unit 1 (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:82-260
2	AVIDIN_1	PS00577	Avidin-like domain signature.	AVID_CHICK	132-146	2	A:174-188

Asymmetric Unit (4, 4)

	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	1	A:17-82 (gaps)	66
1.4	ENSGALT00000003855	4	ENSGALE00000024240	Z:8501440-8501650	211	AVID_CHICK	28-98	71	1	A:83-140 (gaps)	71
1.5	ENSGALT00000003855	5	ENSGALE00000024243	Z:8502076-8502196	121	AVID_CHICK	98-138	41	1	A:140-180	41
1.6a	ENSGALT00000003855	6a	ENSGALE00000024241	Z:8502284-8502409	126	AVID_CHICK	138-152	15	1	A:180-263 (gaps)	84

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:242
 aligned with AVID_CHICK | P02701 from UniProtKB/Swiss-Prot  Length:152

    Alignment length:259
                                        1      8                9               26         27                                                                                                                     147                                                         148 152          
                                     -  |      8         -      | 12        22   |     -    |   32        42        52        62        72        82        92       102       112       122       132       142    |    -         -         -         -         -         -    |   |-         
           AVID_CHICK     - ------------MVHATSPL----------------LLLLLLSLALVAPGLSAR----------KCSLTGKWTNDLGSNMTIGAVNSRGEFTGTYITAVTATSNEIKESPLHGTQNTINKRTQPTFGFTVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVNDIGDDWKATRVGINIFTRL-----------------------------------------------------------RTQKE----------   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee......eeeeeeeeee.hhh.eeeeeeeeee....hhhhhhh.eeeeeeeeee......eeeee....eeee.......eeeeeee............eeeeeee...-----------------..eeeeeeeeee.....eeeeeeeeee....hhhhhhh.eeeeeeeeee.........eeeee....eeee.......eeeeeee............eeeeeee.........eeeeeee.... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------T------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------------------------------------------------AVIDIN_2  PDB: A:82-260 UniProt: 26-149                                                                                                                                                          ------------- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------AVIDIN_1       --------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) ------------Exon 1.1  PDB: A:17-82 (gaps) UniProt: 1-27          Exon 1.4  PDB: A:83-140 (gaps) UniProt: 28-98                          ---------------------------------------Exon 1.6a  PDB: A:180-263 (gaps) UniProt: 138-152                         ---------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------------------------------------------------------------------------Exon 1.5  PDB: A:140-180 UniProt: 98-138 ----------------------------------------------------------------------------------- Transcript 1 (2)
                 2c4i A   5 TQPTFGFTVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVNDIGDDWKATRVGINIFTRLKCSLTGKWTNDLGSNMTIGAVNSRGEFTGTYITAVTATSNEIKESPLHGTQNTI-----------------GSTTVFTGQCFIDRNGKEVLKTMWLLRSSVNDIGDDWKATRVGINIFTRLSARKCSLTGKWTNDLGSNMTIGAVNSRGEFTGTYITAVTATSNEIKESPLHGTQNTINKRTQPTFGFTVNWKFS 273
                                    14        24        34        44        54        64   ||   87        97       107       117       127       | -         -     | 144       154       164       174       184    || 204       214       224       234       244       254       264         
                                                                                          68|                                                  135               140                                              189|                                                                         
                                                                                           82                                                                                                                      200

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 '\|'

(no "SCOP Domain" information available for 2C4I)

(no "CATH Domain" information available for 2C4I)

(no "Pfam Domain" information available for 2C4I)

Asymmetric Unit(hide GO term definitions)

Chain A (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
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		BTN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2c4i)

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	2c4i
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	AVID_CHICK \| P02701
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	AVID_CHICK \| P02701
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

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
1vyo	CRYSTAL STRUCTURE OF AVIDIN
2avi	AVIDIN COMPLEX WITH BIOTIN
2cam	AVIDIN MUTANT (K3E,K9E,R26D,R124L)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 3)

Sites (3, 3)

SS Bonds (2, 2)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 1)

PROSITE Motifs (2, 2)

Exons (4, 4)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (1, 1)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File