1OPB - JenaLib

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Biological Unit 1 (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   THE CRYSTAL STRUCTURES OF HOLO-AND APO-CELLULAR RETINOL BINDING PROTEIN II

Authors :   N. Winter, L. Banaszak

Date :   09 Dec 92 (Deposition) - 31 Oct 93 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)

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

Reference :   N. S. Winter, J. M. Bratt, L. J. Banaszak
Crystal Structures Of Holo And Apo-Cellular Retinol-Binding Protein Ii.
J. Mol. Biol. V. 230 1247 1993
PubMed-ID: 8487303 | Reference-DOI: 10.1006/JMBI.1993.1239
(for further references see the PDB file header)

Molecule 1 - CELLULAR RETINOL BINDING PROTEIN II
	Chains	:	A, B, C, D
	Engineered	:	YES
	Organism Common	:	BLACK RAT
	Organism Scientific	:	RATTUS RATTUS
	Organism Taxid	:	10117

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C
Biological Unit 4 (1x)	:				D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	RET	4	Ligand/Ion	RETINAL

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	RET	1	Ligand/Ion	RETINAL

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	RET	1	Ligand/Ion	RETINAL

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	RET	1	Ligand/Ion	RETINAL

Biological Unit 4 (1, 1)

No.	Name	Count	Type	Full Name
1	RET	1	Ligand/Ion	RETINAL

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:40 , ARG A:58 , LEU A:77 , TRP A:106 , GLN A:108	BINDING SITE FOR RESIDUE RET A 134
2	AC2	SOFTWARE	GLN B:38 , LYS B:40 , THR B:53 , TRP B:106 , GLN B:108	BINDING SITE FOR RESIDUE RET B 134
3	AC3	SOFTWARE	PHE C:16 , GLN C:38 , LYS C:40 , SER C:55 , ARG C:58 , TRP C:106 , GLN C:108	BINDING SITE FOR RESIDUE RET C 134
4	AC4	SOFTWARE	LYS D:40 , THR D:53 , ARG D:58 , TRP D:106 , GLN D:108	BINDING SITE FOR RESIDUE RET D 134

(no "SS Bond" information available for 1OPB)

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

(no "SAP(SNP)/Variant" information available for 1OPB)

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FABP	PS00214	Cytosolic fatty-acid binding proteins signature.	RET2_RAT	7-24	4	A:6-23 B:6-23 C:6-23 D:6-23

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FABP	PS00214	Cytosolic fatty-acid binding proteins signature.	RET2_RAT	7-24	1	A:6-23 - - -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FABP	PS00214	Cytosolic fatty-acid binding proteins signature.	RET2_RAT	7-24	1	- B:6-23 - -

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FABP	PS00214	Cytosolic fatty-acid binding proteins signature.	RET2_RAT	7-24	1	- - C:6-23 -

Biological Unit 4 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FABP	PS00214	Cytosolic fatty-acid binding proteins signature.	RET2_RAT	7-24	1	- - - D:6-23

Asymmetric Unit (4, 16)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENSRNOT00000018755	1	ENSRNOE00000132835	chr8:103665461-103665588	128	RET2_RAT	1-25	25	4	A:1-24 B:1-24 C:1-24 D:1-24	24 24 24 24
1.2	ENSRNOT00000018755	2	ENSRNOE00000213037	chr8:103673980-103674158	179	RET2_RAT	25-84	60	4	A:24-83 B:24-83 C:24-83 D:24-83	60 60 60 60
1.3	ENSRNOT00000018755	3	ENSRNOE00000133487	chr8:103683992-103684093	102	RET2_RAT	85-118	34	4	A:84-117 B:84-117 C:84-117 D:84-117	34 34 34 34
1.4	ENSRNOT00000018755	4	ENSRNOE00000213019	chr8:103685522-103685768	247	RET2_RAT	119-134	16	4	A:118-133 B:118-133 C:118-133 D:118-133	16 16 16 16

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:133
 aligned with RET2_RAT | P06768 from UniProtKB/Swiss-Prot  Length:134

    Alignment length:133
                                    11        21        31        41        51        61        71        81        91       101       111       121       131   
             RET2_RAT     2 TKDQNGTWEMESNENFEGYMKALDIDFATRKIAVRLTQTKIIVQDGDNFKTKTNSTFRNYDLDFTVGVEFDEHTKGLDGRNVKTLVTWEGNTLVCVQKGEKENRGWKQWVEGDKLYLELTCGDQVCRQVFKKK 134
               SCOP domains d1opba_ A: Cellular retinol-binding protein II (CRBP)                                                                                 SCOP domains
               CATH domains 1opbA00 A:1-133  [code=2.40.128.20, no name defined]                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeee.hhhhhhhh...hhhhhhhh.eeeeeeeeee..eeeeeeeee.eeeeeeeee.eeeeeeee....eeeeeeeee...eeeeeee..eeeeeeeeeee..eeeeeeee..eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----FABP  PDB: A:6-23 -------------------------------------------------------------------------------------------------------------- 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)
                 1opb A   1 TKDQNGTWEMESNENFEGYMKALDIDFATRKIAVRLTQTKIIVQDGDNFKTKTNSTFRNYDLDFTVGVEFDEHTKGLDGRNVKTLVTWEGNTLVCVQKGEKENRGWKQWVEGDKLYLELTCGDQVCRQVFKKK 133
                                    10        20        30        40        50        60        70        80        90       100       110       120       130

Chain B from PDB  Type:PROTEIN  Length:133
 aligned with RET2_RAT | P06768 from UniProtKB/Swiss-Prot  Length:134

    Alignment length:133
                                    11        21        31        41        51        61        71        81        91       101       111       121       131   
             RET2_RAT     2 TKDQNGTWEMESNENFEGYMKALDIDFATRKIAVRLTQTKIIVQDGDNFKTKTNSTFRNYDLDFTVGVEFDEHTKGLDGRNVKTLVTWEGNTLVCVQKGEKENRGWKQWVEGDKLYLELTCGDQVCRQVFKKK 134
               SCOP domains d1opbb_ B: Cellular retinol-binding protein II (CRBP)                                                                                 SCOP domains
               CATH domains 1opbB00 B:1-133  [code=2.40.128.20, no name defined]                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeee.hhhhhhhh...hhhhhhhh.eeeeeeeeee..eeeeeeeee.eeeeeeeee.eeeeeeee....eeeeeeeee...eeeeeee..eeeeeeeeeee..eeeeeeee..eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----FABP  PDB: B:6-23 -------------------------------------------------------------------------------------------------------------- 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)
                 1opb B   1 TKDQNGTWEMESNENFEGYMKALDIDFATRKIAVRLTQTKIIVQDGDNFKTKTNSTFRNYDLDFTVGVEFDEHTKGLDGRNVKTLVTWEGNTLVCVQKGEKENRGWKQWVEGDKLYLELTCGDQVCRQVFKKK 133
                                    10        20        30        40        50        60        70        80        90       100       110       120       130

Chain C from PDB  Type:PROTEIN  Length:133
 aligned with RET2_RAT | P06768 from UniProtKB/Swiss-Prot  Length:134

    Alignment length:133
                                    11        21        31        41        51        61        71        81        91       101       111       121       131   
             RET2_RAT     2 TKDQNGTWEMESNENFEGYMKALDIDFATRKIAVRLTQTKIIVQDGDNFKTKTNSTFRNYDLDFTVGVEFDEHTKGLDGRNVKTLVTWEGNTLVCVQKGEKENRGWKQWVEGDKLYLELTCGDQVCRQVFKKK 134
               SCOP domains d1opbc_ C: Cellular retinol-binding protein II (CRBP)                                                                                 SCOP domains
               CATH domains 1opbC00 C:1-133  [code=2.40.128.20, no name defined]                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeee.hhhhhhhh...hhhhhhhh.eeeeeeeeee..eeeeeeeee.eeeeeeeee.eeeeeeee....eeeeeeeee...eeeeeee..eeeeeeeeeee..eeeeeeee..eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----FABP  PDB: C:6-23 -------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: C:1-24   -----------------------------------------------------------Exon 1.3  PDB: C:84-117           Exon 1.4         Transcript 1 (1)
           Transcript 1 (2) -----------------------Exon 1.2  PDB: C:24-83 UniProt: 25-84                       -------------------------------------------------- Transcript 1 (2)
                 1opb C   1 TKDQNGTWEMESNENFEGYMKALDIDFATRKIAVRLTQTKIIVQDGDNFKTKTNSTFRNYDLDFTVGVEFDEHTKGLDGRNVKTLVTWEGNTLVCVQKGEKENRGWKQWVEGDKLYLELTCGDQVCRQVFKKK 133
                                    10        20        30        40        50        60        70        80        90       100       110       120       130

Chain D from PDB  Type:PROTEIN  Length:133
 aligned with RET2_RAT | P06768 from UniProtKB/Swiss-Prot  Length:134

    Alignment length:133
                                    11        21        31        41        51        61        71        81        91       101       111       121       131   
             RET2_RAT     2 TKDQNGTWEMESNENFEGYMKALDIDFATRKIAVRLTQTKIIVQDGDNFKTKTNSTFRNYDLDFTVGVEFDEHTKGLDGRNVKTLVTWEGNTLVCVQKGEKENRGWKQWVEGDKLYLELTCGDQVCRQVFKKK 134
               SCOP domains d1opbd_ D: Cellular retinol-binding protein II (CRBP)                                                                                 SCOP domains
               CATH domains 1opbD00 D:1-133  [code=2.40.128.20, no name defined]                                                                                  CATH domains
           Pfam domains (1) ----Lipocalin-1opbD01 D:5-133                                                                                                         Pfam domains (1)
           Pfam domains (2) ----Lipocalin-1opbD02 D:5-133                                                                                                         Pfam domains (2)
           Pfam domains (3) ----Lipocalin-1opbD03 D:5-133                                                                                                         Pfam domains (3)
           Pfam domains (4) ----Lipocalin-1opbD04 D:5-133                                                                                                         Pfam domains (4)
         Sec.struct. author .eeeeeeeeeeeee.hhhhhhhh...hhhhhhhh.eeeeeeeeee..eeeeeeeee.eeeeeeeee.eeeeeeee....eeeeeeeee...eeeeeee..eeeeeeeeeee..eeeeeeee..eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----FABP  PDB: D:6-23 -------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: D:1-24   -----------------------------------------------------------Exon 1.3  PDB: D:84-117           Exon 1.4         Transcript 1 (1)
           Transcript 1 (2) -----------------------Exon 1.2  PDB: D:24-83 UniProt: 25-84                       -------------------------------------------------- Transcript 1 (2)
                 1opb D   1 TKDQNGTWEMESNENFEGYMKALDIDFATRKIAVRLTQTKIIVQDGDNFKTKTNSTFRNYDLDFTVGVEFDEHTKGLDGRNVKTLVTWEGNTLVCVQKGEKENRGWKQWVEGDKLYLELTCGDQVCRQVFKKK 133
                                    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)
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	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: Lipocalins (514)

Superfamily: Lipocalins (514)

Family: Fatty acid binding protein-like (183)

Protein domain: Cellular retinol-binding protein II (CRBP) (11)

Norway rat (Rattus norvegicus) [TaxId: 10116] (9)

1a	d1opba_	A:
1b	d1opbb_	B:
1c	d1opbc_	C:
1d	d1opbd_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: Lipocalin (526)

Homologous Superfamily: [code=2.40.128.20, no name defined] (352)

Black rat (Rattus rattus) (4)

1a	1opbA00	A:1-133
1b	1opbB00	B:1-133
1c	1opbC00	C:1-133
1d	1opbD00	D:1-133

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Calycin (163)

Family: Lipocalin (123)

Rattus norvegicus (Rat) (11)

1a	Lipocalin-1opbD01	D:5-133
1b	Lipocalin-1opbD02	D:5-133
1c	Lipocalin-1opbD03	D:5-133
1d	Lipocalin-1opbD04	D:5-133

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (RET2_RAT | P06768)

molecular function
	GO:0008289	lipid binding	Interacting selectively and non-covalently with a lipid.
	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: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:0042572	retinol metabolic process	The chemical reactions and pathways involving retinol, one of the three compounds that makes up vitamin A.
	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.
	GO:0006776	vitamin A metabolic process	The chemical reactions and pathways involving any of the vitamin A compounds, retinol, retinal (retinaldehyde) and retinoic acid, all of which are derivatives of beta-carotene.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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