1GGL - JenaLib

Title :   HUMAN CELLULAR RETINOL BINDING PROTEIN III

Authors :   V. Calderone, G. Zanotti, C. Folli, S. Ottonello, A. Bolchi, M. Stoppini, R. Berni

Date :   23 Aug 00 (Deposition) - 07 Mar 01 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.31

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

Keywords :   Carrier, Retinol Binding Protein, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Folli, V. Calderone, S. Ottonello, A. Bolchi, G. Zanotti, M. Stoppini, R. Berni
Identification, Retinoid Binding, And X-Ray Analysis Of A Human Retinol-Binding Protein.
Proc. Natl. Acad. Sci. Usa V. 98 3710 2001
PubMed-ID: 11274389 | Reference-DOI: 10.1073/PNAS.061455898
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (3, 6)

Asymmetric Unit (3, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_049013	D	19	N	RET5_HUMAN	Polymorphism	10963	A/B	D	18	N
2	UniProt	VAR_034445	E	70	Q	RET5_HUMAN	Polymorphism	7969705	A/B	E	69	Q
3	UniProt	VAR_034446	M	115	L	RET5_HUMAN	Polymorphism	2290237	A/B	M	114	L

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

Biological Unit 1 (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_049013	D	19	N	RET5_HUMAN	Polymorphism	10963	A	D	18	N
2	UniProt	VAR_034445	E	70	Q	RET5_HUMAN	Polymorphism	7969705	A	E	69	Q
3	UniProt	VAR_034446	M	115	L	RET5_HUMAN	Polymorphism	2290237	A	M	114	L

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

Biological Unit 2 (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_049013	D	19	N	RET5_HUMAN	Polymorphism	10963	B	D	18	N
2	UniProt	VAR_034445	E	70	Q	RET5_HUMAN	Polymorphism	7969705	B	E	69	Q
3	UniProt	VAR_034446	M	115	L	RET5_HUMAN	Polymorphism	2290237	B	M	114	L

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

PROSITE Motifs (0, 0)

Exons (4, 8)

Sequences/Alignments

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:134
 aligned with RET5_HUMAN | P82980 from UniProtKB/Swiss-Prot  Length:135

    Alignment length:134
                                    11        21        31        41        51        61        71        81        91       101       111       121       131    
           RET5_HUMAN     2 PPNLTGYYRFVSQKNMEDYLQALNISLAVRKIALLLKPDKEIEHQGNHMTVRTLSTFRNYTVQFDVGVEFEEDLRSVDGRKCQTIVTWEEEHLVCVQKGEVPNRGWRHWLEGEMLYLELTARDAVCEQVFRKVR 135
               SCOP domains d1ggla_ A: Cellular retinol-binding protein III                                                                                        SCOP domains
               CATH domains 1gglA00 A:1-134  [code=2.40.128.20, no name defined]                                                                                   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeehhhhhhhhh........hhhhh..eeeeee...eeeeeee.....eeeeee....eeee.......eeeeeeee....eeeeee......eeeeeee..eeeeeeee..eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -----------------N--------------------------------------------------Q--------------------------------------------L-------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: A:1-24   -----------------------------------------------------------Exon 1.3  PDB: A:84-117           Exon 1.4          Transcript 1 (1)
           Transcript 1 (2) -----------------------Exon 1.2  PDB: A:24-83 UniProt: 25-84                       --------------------------------------------------- Transcript 1 (2)
                 1ggl A   1 PPNLTGYYRFVSQKNMEDYLQALNISLAVRKIALLLKPDKEIEHQGNHMTVRTLSTFRNYTVQFDVGVEFEEDLRSVDGRKCQTIVTWEEEHLVCVQKGEVPNRGWRHWLEGEMLYLELTARDAVCEQVFRKVH 134
                                    10        20        30        40        50        60        70        80        90       100       110       120       130

Chain B from PDB  Type:PROTEIN  Length:134
 aligned with RET5_HUMAN | P82980 from UniProtKB/Swiss-Prot  Length:135

    Alignment length:134
                                    11        21        31        41        51        61        71        81        91       101       111       121       131    
           RET5_HUMAN     2 PPNLTGYYRFVSQKNMEDYLQALNISLAVRKIALLLKPDKEIEHQGNHMTVRTLSTFRNYTVQFDVGVEFEEDLRSVDGRKCQTIVTWEEEHLVCVQKGEVPNRGWRHWLEGEMLYLELTARDAVCEQVFRKVR 135
               SCOP domains d1gglb_ B: Cellular retinol-binding protein III                                                                                        SCOP domains
               CATH domains 1gglB00 B:1-134  [code=2.40.128.20, no name defined]                                                                                   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeehhhhhhhhh..hhhhhhh......eeeeeee..eeeeeee....eeeeeee....eeee.......eeeeeeee....eeeeee......eeeeeee..eeeeeeee..eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -----------------N--------------------------------------------------Q--------------------------------------------L-------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: B:1-24   -----------------------------------------------------------Exon 1.3  PDB: B:84-117           Exon 1.4          Transcript 1 (1)
           Transcript 1 (2) -----------------------Exon 1.2  PDB: B:24-83 UniProt: 25-84                       --------------------------------------------------- Transcript 1 (2)
                 1ggl B   1 PPNLTGYYRFVSQKNMEDYLQALNISLAVRKIALLLKPDKEIEHQGNHMTVRTLSTFRNYTVQFDVGVEFEEDLRSVDGRKCQTIVTWEEEHLVCVQKGEVPNRGWRHWLEGEMLYLELTARDAVCEQVFRKVH 134
                                    10        20        30        40        50        60        70        80        90       100       110       120       130

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 '\|'

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (9, 9)

Asymmetric Unit(hide GO term definitions)

Chain A,B (RET5_HUMAN | P82980)

molecular function
	GO:0008289	lipid binding	Interacting selectively and non-covalently with a lipid.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0016918	retinal binding	Interacting selectively and non-covalently with retinal, one of the forms of vitamin A. Retinal plays an important role in the visual process in most vertebrates, combining with opsins to form visual pigments in the retina.
	GO:0005501	retinoid binding	Interacting selectively and non-covalently with retinoids, any member of a class of isoprenoids that contain or are derived from four prenyl groups linked head-to-tail. Retinoids include retinol and retinal and structurally similar natural derivatives or synthetic compounds, but need not have vitamin A activity.
	GO:0019841	retinol binding	Interacting selectively and non-covalently with retinol, vitamin A1, 2,6,6-trimethyl-1-(9'-hydroxy-3',7'-dimethylnona-1',3',5',7'-tetraenyl)cyclohex-1-ene, one of the three components that makes up vitamin A. Retinol is an intermediate in the vision cycle and it also plays a role in growth and differentiation.
	GO:0005215	transporter activity	Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells.
biological process
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.

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