4GOK - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   THE CRYSTAL STRUCTURE OF ARL2GPPNHP IN COMPLEX WITH UNC119A

Authors :   S. Ismail, Y. Xiang-Chen, M. Miertzschke, I. Vetter, C. Koerner, A. Wit

Date :   20 Aug 12 (Deposition) - 19 Sep 12 (Release) - 31 Oct 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

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

Keywords :   Small G Proteins, Arl, Arf, Gdi-Like Solubilizing Factors, Cilia, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. A. Ismail, Y. X. Chen, M. Miertzschke, I. R. Vetter, C. Koerner, A. Wittinghofer
Structural Basis For Arl3-Specific Release Of Myristoylated Ciliary Cargo From Unc119.
Embo J. V. 31 4085 2012
PubMed-ID: 22960633 | Reference-DOI: 10.1038/EMBOJ.2012.257

Molecule 1 - ADP-RIBOSYLATION FACTOR-LIKE PROTEIN 2
	Chains	:	B, A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	ARL2
	Mutation	:	YES
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

Molecule 2 - PROTEIN UNC-119 HOMOLOG A
	Chains	:	G, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	UNC119, RG4
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	RETINAL PROTEIN 4, HRG4

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	GNP	2	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2	MG	2	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	GNP	1	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	GNP	1	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP B:25 , ASN B:26 , ALA B:27 , GLY B:28 , LYS B:29 , THR B:30 , THR B:31 , THR B:47 , GLY B:69 , ASN B:125 , LYS B:126 , ASP B:128 , LEU B:129 , SER B:158 , ALA B:159 , VAL B:160 , MG B:202 , HOH B:301 , HOH B:302	BINDING SITE FOR RESIDUE GNP B 201
2	AC2	SOFTWARE	THR B:30 , THR B:47 , ASP B:66 , GNP B:201 , HOH B:301 , HOH B:302	BINDING SITE FOR RESIDUE MG B 202
3	AC3	SOFTWARE	ASP A:25 , ASN A:26 , ALA A:27 , GLY A:28 , LYS A:29 , THR A:30 , THR A:31 , THR A:47 , GLY A:69 , ASN A:125 , LYS A:126 , ASP A:128 , LEU A:129 , SER A:158 , ALA A:159 , VAL A:160 , MG A:202 , HOH A:301 , HOH A:302 , HOH A:303	BINDING SITE FOR RESIDUE GNP A 201
4	AC4	SOFTWARE	THR A:30 , THR A:47 , ASP A:66 , GNP A:201 , HOH A:301 , HOH A:302	BINDING SITE FOR RESIDUE MG A 202

(no "SS Bond" information available for 4GOK)

Asymmetric Unit

No.	Residues
1	Pro G:108	-	Pro G:109
2	Pro C:108	-	Pro C:109

(no "SAP(SNP)/Variant" information available for 4GOK)

(no "PROSITE Motif" information available for 4GOK)

(no "Exon" information available for 4GOK)

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:158
                                                                                                                                                                                              
               SCOP domains d4goka_ A: ADP-ribosylation factor                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....hhhhhhhhh........eeeeeeee..eeeeeeee.....hhhhhhhhh....eeeeeee..hhhhhhhhhhhhhhhhhhhhhh..eeeeeee........hhhhhhhhhhhhhh....eeeee........hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gok A  17 LRLLMLGLDNAGKTTILKKFNTISPTLGFNIKTLEHRGFKLNIWDVGGLKSLRSYWRNYFESTDGLIWVVDSADRQRMQDCQRELQSLLVEERLAGATLLIFANKQDLPGALSCNAIQEALELDSIRSHHWRIQGCSAVTGEDLLPGIDWLLDDISSR 179
                                    26        36||      51        61        71        81        91       101       111       121       131       141       151       161       171        
                                               37|                                                                                                                                        
                                                43

Chain B from PDB  Type:PROTEIN  Length:157
                                                                                                                                                                                             
               SCOP domains d4gokb_ B: ADP-ribosylation factor                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....hhhhhhhhh.......eeeeeeee..eeeeeeee.....hhhhhhhhh....eeeeeee..hhhhhhhhhhhhhhhhhhhhhh..eeeeeee........hhhhhhhhhhhhhh....eeeee........hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gok B  17 LRLLMLGLDNAGKTTILKKFTISPTLGFNIKTLEHRGFKLNIWDVGGLKSLRSYWRNYFESTDGLIWVVDSADRQRMQDCQRELQSLLVEERLAGATLLIFANKQDLPGALSCNAIQEALELDSIRSHHWRIQGCSAVTGEDLLPGIDWLLDDISSR 179
                                    26        36|       52        62        72        82        92       102       112       122       132       142       152       162       172       
                                              36|                                                                                                                                        
                                               43

Chain C from PDB  Type:PROTEIN  Length:161
                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhh..........hhhhh....eeeeeeeee.....eeeeee.......eeeee.hhhhhhh..eeeeeeee.....eeeeeeeeeeee..eeeeeeeeeeeee....eeeeeeee.hhhhhhhhhhh...eeeeeeeee..eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gok C  59 PIGPEDVLGLQRITGDYLCSPEENIYKIDFVRFKIRDMDSGTVLFEIKKPPNAGRFVRYQFTPAFLRLRQVGATVEFTVGDKPVNNFRMIERHYFRNQLLKSFDFHFGFCIPSSKNTCEHIYLSEELISEMIRHPYETQSDSFYFVDDRLVMHNKADYSYS 237
                                    68        78        88        98       108||     132       142       152       162       172       182       192 ||    206       216       226       236 
                                                                            109|                                                                   194|                                      
                                                                             124                                                                    199

Chain G from PDB  Type:PROTEIN  Length:161
                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhh..........hhhhh....eeeeeeeee.....eeeeee.......eeeee.hhhhhhh..eeeeeeee.....eeeeeeeeeeee..eeeeeeeeeeeee....eeeeeeee.hhhhhhhhhhh...eeeeeeeee..eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gok G  59 PIGPEDVLGLQRITGDYLCSPEENIYKIDFVRFKIRDMDSGTVLFEIKKPPNAGRFVRYQFTPAFLRLRQVGATVEFTVGDKPVNNFRMIERHYFRNQLLKSFDFHFGFCIPSSKNTCEHIYLSEELISEMIRHPYETQSDSFYFVDDRLVMHNKADYSYS 237
                                    68        78        88        98       108||     132       142       152       162       172       182       192 ||    206       216       226       236 
                                                                            109|                                                                   194|                                      
                                                                             124                                                                    199

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: Alpha and beta proteins (a/b) (23833)

Fold: P-loop containing nucleoside triphosphate hydrolases (2083)

Superfamily: P-loop containing nucleoside triphosphate hydrolases (2083)

Family: G proteins (693)

Protein domain: ADP-ribosylation factor (40)

Mouse (Mus musculus), ARL2 [TaxId: 10090] (4)

1a	d4goka_	A:
1b	d4gokb_	B:

(no "CATH Domain" information available for 4GOK)

(no "Pfam Domain" information available for 4GOK)

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Cis Peptide Bonds
		Pro C:108 - Pro C:109	[ RasMol ]
		Pro G:108 - Pro G:109	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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	4gok
		Family and Domain Information	:	ProDom \| SYSTERS
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		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
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	ARL2_MOUSE \| Q9D0J4
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		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	U119A_HUMAN \| Q13432
		Comparative Protein Structure Models	:	ModBase
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		Protein-protein Interaction	:	DIP
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		Interatomic Contacts of Structural Units	:	CSU
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	ARL2_MOUSE \| Q9D0J4
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	U119A_HUMAN \| Q13432
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	ARL2_MOUSE \| Q9D0J4	:	1ksg 1ksh 1ksj
	U119A_HUMAN \| Q13432	:	3gqq 3rbq 4goj 5l7k

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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SCOP Domains (1, 2)

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Gene Ontology (40, 45)

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