3VHM - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF NPC-BIOTIN-AVIDIN COMPLEX

Authors :   T. Terai, E. Maki, S. Sugiyama, Y. Takahashi, H. Matsumura, Y. Mori, T. N

Date :   29 Aug 11 (Deposition) - 28 Dec 11 (Release) - 28 Dec 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym./Biol. Unit : A,B,C,D

Keywords :   Beta Barrel, Biotin-Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Terai, E. Maki, S. Sugiyama, Y. Takahashi, H. Matsumura, Y. Mori, T. Nagano
Rational Development Of Caged-Biotin Protein-Labeling Agent And Some Applications In Live Cells
Chem. Biol. V. 18 1261 2011
PubMed-ID: 22035795 | Reference-DOI: 10.1016/J.CHEMBIOL.2011.09.007

Molecule 1 - AVIDIN
	Chains	:	A, B, C, D
	Fragment	:	UNP RESIDUES 25-147
	Organism Common	:	CHICKEN
	Organism Scientific	:	GALLUS GALLUS
	Organism Taxid	:	9031

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 14)

No.	Name	Count	Type	Full Name
1	NAG	4	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
2	NPK	4	Ligand/Ion	5-[(3AS,4R,6AR)-1-{[(1R)-1-(6-NITRO-1,3-BENZODIOXOL-5-YL)ETHOXY]CARBONYL}-2-OXOHEXAHYDRO-1H-THIENO[3,4-D]IMIDAZOL-4-YL]PENTANOIC ACID
3	SO4	6	Ligand/Ion	SULFATE ION

Asymmetric Unit (14, 14)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASN A:12 , ASP A:13 , LEU A:14 , SER A:16 , TYR A:33 , THR A:35 , VAL A:37 , THR A:38 , ALA A:39 , TRP A:70 , SER A:73 , SER A:75 , TRP A:97 , ILE A:117 , ASN A:118 , HOH A:124 , GLY C:107 , TRP C:110 , HOH C:159	BINDING SITE FOR RESIDUE NPK A 1124
02	AC2	SOFTWARE	LYS A:9 , GLY A:15 , ASN A:17 , ILE A:34 , LEU A:123	BINDING SITE FOR RESIDUE NAG A 1125
03	AC3	SOFTWARE	ARG A:2 , LYS A:90 , GLU A:91 , ARG A:122 , HOH A:138 , LYS D:9 , HOH D:173	BINDING SITE FOR RESIDUE SO4 A 1126
04	AC4	SOFTWARE	ARG A:59 , THR A:60	BINDING SITE FOR RESIDUE SO4 A 1127
05	AC5	SOFTWARE	ASN B:12 , LEU B:14 , SER B:16 , TYR B:33 , THR B:35 , VAL B:37 , THR B:38 , ALA B:39 , TRP B:70 , SER B:73 , SER B:75 , TRP B:97 , ILE B:117 , ASN B:118 , ILE B:119 , HOH B:142 , HOH B:194 , TRP D:110	BINDING SITE FOR RESIDUE NPK B 1124
06	AC6	SOFTWARE	GLY B:15 , ASN B:17 , ILE B:34	BINDING SITE FOR RESIDUE NAG B 1125
07	AC7	SOFTWARE	LYS B:9 , ARG C:2 , LYS C:90 , GLU C:91 , ARG C:122 , HOH C:149 , HOH C:185	BINDING SITE FOR RESIDUE SO4 B 1126
08	AC8	SOFTWARE	ARG B:59 , THR B:60 , ARG D:87	BINDING SITE FOR RESIDUE SO4 B 1127
09	AC9	SOFTWARE	GLY A:107 , TRP A:110 , ASN C:12 , LEU C:14 , SER C:16 , TYR C:33 , THR C:35 , THR C:38 , ALA C:39 , THR C:40 , TRP C:70 , SER C:75 , TRP C:97 , LEU C:99 , ILE C:117 , ASN C:118 , HOH C:181	BINDING SITE FOR RESIDUE NPK C 1124
10	BC1	SOFTWARE	GLY C:15 , ASN C:17	BINDING SITE FOR RESIDUE NAG C 1125
11	BC2	SOFTWARE	ARG C:59 , THR C:60 , HOH C:154	BINDING SITE FOR RESIDUE SO4 C 1127
12	BC3	SOFTWARE	TRP B:110 , ASN D:12 , ASP D:13 , LEU D:14 , SER D:16 , TYR D:33 , THR D:35 , VAL D:37 , THR D:38 , ALA D:39 , TRP D:70 , SER D:73 , SER D:75 , TRP D:97 , ILE D:117 , ASN D:118 , ILE D:119 , HOH D:139 , HOH D:167	BINDING SITE FOR RESIDUE NPK D 1124
13	BC4	SOFTWARE	GLY D:15 , ASN D:17 , ILE D:34	BINDING SITE FOR RESIDUE NAG D 1125
14	BC5	SOFTWARE	ARG D:59 , THR D:60 , HOH D:152	BINDING SITE FOR RESIDUE SO4 D 1126

Asymmetric/Biological Unit

No.	Residues
1	A:4	-	A:83
2	B:4	-	B:83
3	C:4	-	C:83
4	D:4	-	D:83

(no "Cis Peptide Bond" information available for 3VHM)

Asymmetric/Biological Unit (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/C/D	I	34	T
	* ID not provided by source

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

Asymmetric/Biological Unit (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 C:2-123
2	AVIDIN_1	PS00577	Avidin-like domain signature.	AVID_CHICK	132-146	4	A:108-122 B:108-122 C:108-122 D:108-122

Asymmetric/Biological Unit (4, 16)

	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	4	A:1-3 B:3-3 C:1-3 D:3-3	3 1 3 1
1.4	ENSGALT00000003855	4	ENSGALE00000024240	Z:8501440-8501650	211	AVID_CHICK	28-98	71	4	A:4-74 B:4-74 C:4-74 D:4-74	71 71 71 71
1.5	ENSGALT00000003855	5	ENSGALE00000024243	Z:8502076-8502196	121	AVID_CHICK	98-138	41	4	A:74-114 B:74-114 C:74-114 D:74-114	41 41 41 41
1.6a	ENSGALT00000003855	6a	ENSGALE00000024241	Z:8502284-8502409	126	AVID_CHICK	138-152	15	4	A:114-123 B:114-123 C:114-123 D:114-123	10 10 10 10

Asymmetric/Biological 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 d3vhma_ A: automated matches                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeee.....eeee.......eeeeeee............eeeeeee.hhhhh...eeeeee.......eeeeeeeeee.....eeeeeeeeee....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)
                 3vhm A   1 ARKCSLTGKWTNDLGSNMTIGAVNSRGEFTGTYITAVTATSNEIKESPLHGTQNTINKRTQPTFGFTVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVNDIGDDWKATRVGINIFTRL 123
                                    10        20        30        40        50        60        70        80        90       100       110       120

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 d3vhmb_ B: automated matches                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee.....eeee.......eeeeeee............eeeeeee.hhhhh...eeeeeee......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: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)
                 3vhm B   3 KCSLTGKWTNDLGSNMTIGAVNSRGEFTGTYITAVTATSNEIKESPLHGTQNTINKRTQPTFGFTVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVNDIGDDWKATRVGINIFTRL 123
                                    12        22        32        42        52        62        72        82        92       102       112       122

Chain C 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 d3vhmc_ C: automated matches                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeee.....eeee.......eeeeeee............eeeeeee.hhhhh...eeeeeee......eeeeeeeeee.....eeeeeeeeee....hhhhhhh.eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------T----------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -AVIDIN_2  PDB: C:2-123 UniProt: 26-149                                                                                     PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------AVIDIN_1       - PROSITE (2)
           Transcript 1 (1) 1.1Exon 1.4  PDB: C:4-74 UniProt: 28-98                                   ---------------------------------------Exon 1.6a  Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------Exon 1.5  PDB: C:74-114 UniProt: 98-138  --------- Transcript 1 (2)
                 3vhm C   1 ARKCSLTGKWTNDLGSNMTIGAVNSRGEFTGTYITAVTATSNEIKESPLHGTQNTINKRTQPTFGFTVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVNDIGDDWKATRVGINIFTRL 123
                                    10        20        30        40        50        60        70        80        90       100       110       120

Chain D 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 d3vhmd_ D: automated matches                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee.....eeee.......eeeeeee............eeeeeee.hhhhh...eeeeeee......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: D:4-74 UniProt: 28-98                                   ---------------------------------------Exon 1.6a  Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------Exon 1.5  PDB: D:74-114 UniProt: 98-138  --------- Transcript 1 (2)
                 3vhm D   3 KCSLTGKWTNDLGSNMTIGAVNSRGEFTGTYITAVTATSNEIKESPLHGTQNTINKRTQPTFGFTVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVNDIGDDWKATRVGINIFTRL 123
                                    12        22        32        42        52        62        72        82        92       102       112       122

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/Biological 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	d3vhma_	A:
1b	d3vhmb_	B:
1c	d3vhmc_	C:
1d	d3vhmd_	D:

(no "CATH Domain" information available for 3VHM)

(no "Pfam Domain" information available for 3VHM)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (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/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3vhm)

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	3vhm
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	AVID_CHICK \| P02701
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 14)

Sites (14, 14)

SS Bonds (4, 4)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 4)

PROSITE Motifs (2, 6)

Exons (4, 16)

Sequences/Alignments

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SCOP Domains (1, 4)

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