1Z6Y - JenaLib

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Title :   STRUCTURE OF HUMAN ADP-RIBOSYLATION FACTOR-LIKE 5

Authors :   J. Choe, A. Atanassova, C. Arrowsmith, A. Edwards, M. Sundstrom, A. Bochkarev, H. Park, Structural Genomics Consortium (Sgc)

Date :   23 Mar 05 (Deposition) - 05 Apr 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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

Keywords :   Gdp-Binding, Membrane Trafficking, Structural Genomics, Structural Genomics Consortium, Sgc, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Atanassova, J. Choe, C. Arrowsmith, A. Edwards, M. Sundstrom, A. Bochkarev, H. Park
Structure Of Human Adp-Ribosylation Factor-Like 5
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - ADP-RIBOSYLATION FACTOR-LIKE PROTEIN 5
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET28
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	ARL5, ARFLP5
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	GDP	2	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	GDP	1	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	GDP	1	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:26 , ALA A:27 , GLY A:28 , LYS A:29 , THR A:30 , THR A:31 , ASN A:125 , LYS A:126 , ASP A:128 , CYS A:158 , ALA A:159 , LEU A:160 , HOH A:224 , HOH A:328 , GLN B:140	BINDING SITE FOR RESIDUE GDP A 180
2	AC2	SOFTWARE	GLN A:140 , ASN B:26 , ALA B:27 , GLY B:28 , LYS B:29 , THR B:30 , THR B:31 , ASN B:125 , LYS B:126 , ASP B:128 , CYS B:158 , ALA B:159 , LEU B:160 , HOH B:238 , HOH B:242 , HOH B:247 , HOH B:329	BINDING SITE FOR RESIDUE GDP B 180

(no "SS Bond" information available for 1Z6Y)

(no "Cis Peptide Bond" information available for 1Z6Y)

(no "SAP(SNP)/Variant" information available for 1Z6Y)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ARF	PS51417	small GTPase Arf family profile.	ARL5A_HUMAN	10-176	2	A:10-175 B:10-175

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ARF	PS51417	small GTPase Arf family profile.	ARL5A_HUMAN	10-176	1	A:10-175 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ARF	PS51417	small GTPase Arf family profile.	ARL5A_HUMAN	10-176	1	- B:10-175

Asymmetric Unit (6, 12)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1d	ENST00000295087	1d	ENSE00001364904	chr2:152685002-152684645	358	ARL5A_HUMAN	1-16	16	2	A:3-16 B:3-16	14 14
1.3a	ENST00000295087	3a	ENSE00001655660	chr2:152671713-152671653	61	ARL5A_HUMAN	16-36	21	2	A:16-36 B:16-36	21 21
1.4	ENST00000295087	4	ENSE00001724503	chr2:152670830-152670683	148	ARL5A_HUMAN	36-85	50	2	A:36-85 (gaps) B:36-85 (gaps)	50 50
1.5	ENST00000295087	5	ENSE00001070294	chr2:152668954-152668871	84	ARL5A_HUMAN	86-113	28	2	A:86-113 B:86-113	28 28
1.7	ENST00000295087	7	ENSE00001795074	chr2:152663486-152663335	152	ARL5A_HUMAN	114-164	51	2	A:114-164 B:114-164	51 51
1.8d	ENST00000295087	8d	ENSE00001827771	chr2:152659838-152655316	4523	ARL5A_HUMAN	164-179	16	2	A:164-175 B:164-175	12 12

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
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Chain A from PDB  Type:PROTEIN  Length:169
 aligned with ARL5A_HUMAN | Q9Y689 from UniProtKB/Swiss-Prot  Length:179

    Alignment length:173
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172   
          ARL5A_HUMAN     3 ILFTRIWRLFNHQEHKVIIVGLDNAGKTTILYQFSMNEVVHTSPTIGSNVEEIVINNTRFLMWDIGGQESLRSSWNTYYTNTEFVIVVVDSTDRERISVTREELYKMLAHEDLRKAGLLIFANKQDVKECMTVAEISQFLKLTSIKDHQWHIQACCALTGEGLCQGLEWMMSR 175
               SCOP domains d1z6ya_ A: automated matches                                                                                                                                                  SCOP domains
               CATH domains 1z6yA00 A:3-175 P-loop containing nucleotide triphosphate hydrolases                                                                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh...eeeeeeee...hhhhhhhhh.....eeeee......eeeee..eeeeeeeehhhhh...----......eeeeeee.....hhhhhhhhhhhhhhhhhhh..eeeeeee........hhhhhh...hhhhh....eeeee.......hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------ARF  PDB: A:10-175 UniProt: 10-176                                                                                                                                     PROSITE
           Transcript 1 (1) Exon 1.1d     -------------------Exon 1.4  PDB: A:36-85 (gaps) UniProt: 36-85      Exon 1.5  PDB: A:86-113     Exon 1.7  PDB: A:114-164 UniProt: 114-164          ----------- Transcript 1 (1)
           Transcript 1 (2) -------------Exon 1.3a            -------------------------------------------------------------------------------------------------------------------------------Exon 1.8d    Transcript 1 (2)
                 1z6y A   3 ILFTRIWRLFNHQEHKVIIVGLDNAGKTTILYQFSMNEVVHTSPTIGSNVEEIVINNTRFLMWDIGGQESLRS----YYTNTEFVIVVVDSTDRERISVTREELYKMLAHEDLRKAGLLIFANKQDVKECMTVAEISQFLKLTSIKDHQWHIQACCALTGEGLCQGLEWMMSR 175
                                    12        22        32        42        52        62        72  |    |82        92       102       112       122       132       142       152       162       172   
                                                                                                   75   80

Chain B from PDB  Type:PROTEIN  Length:169
 aligned with ARL5A_HUMAN | Q9Y689 from UniProtKB/Swiss-Prot  Length:179

    Alignment length:173
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172   
          ARL5A_HUMAN     3 ILFTRIWRLFNHQEHKVIIVGLDNAGKTTILYQFSMNEVVHTSPTIGSNVEEIVINNTRFLMWDIGGQESLRSSWNTYYTNTEFVIVVVDSTDRERISVTREELYKMLAHEDLRKAGLLIFANKQDVKECMTVAEISQFLKLTSIKDHQWHIQACCALTGEGLCQGLEWMMSR 175
               SCOP domains d1z6yb_ B: automated matches                                                                                                                                                  SCOP domains
               CATH domains 1z6yB00 B:3-175 P-loop containing nucleotide triphosphate hydrolases                                                                                                          CATH domains
           Pfam domains (1) --Arf-1z6yB01 B:5-175                                                                                                                                                         Pfam domains (1)
           Pfam domains (2) --Arf-1z6yB02 B:5-175                                                                                                                                                         Pfam domains (2)
         Sec.struct. author hhhhhhhhhhh...eeeeeeee...hhhhhhhhhhh...eeeee......eeeee..eeeeeeeehhhhhhh.----......eeeeeee.....hhhhhhhhhhhhhhhhhhh..eeeeeee........hhhhhh...hhhhh....eeeee.......hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------ARF  PDB: B:10-175 UniProt: 10-176                                                                                                                                     PROSITE
           Transcript 1 (1) Exon 1.1d     -------------------Exon 1.4  PDB: B:36-85 (gaps) UniProt: 36-85      Exon 1.5  PDB: B:86-113     Exon 1.7  PDB: B:114-164 UniProt: 114-164          ----------- Transcript 1 (1)
           Transcript 1 (2) -------------Exon 1.3a            -------------------------------------------------------------------------------------------------------------------------------Exon 1.8d    Transcript 1 (2)
                 1z6y B   3 ILFTRIWRLFNHQEHKVIIVGLDNAGKTTILYQFSMNEVVHTSPTIGSNVEEIVINNTRFLMWDIGGQESLRS----YYTNTEFVIVVVDSTDRERISVTREELYKMLAHEDLRKAGLLIFANKQDVKECMTVAEISQFLKLTSIKDHQWHIQACCALTGEGLCQGLEWMMSR 175
                                    12        22        32        42        52        62        72  |    |82        92       102       112       122       132       142       152       162       172   
                                                                                                   75   80

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

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

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

Family: automated matches (303)

Protein domain: automated matches (303)

Human (Homo sapiens) [TaxId: 9606] (86)

1a	d1z6ya_	A:
1b	d1z6yb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: P-loop containing nucleotide triphosphate hydrolases (1378)

Human (Homo sapiens) (413)

1a	1z6yA00	A:3-175
1b	1z6yB00	B:3-175

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: Arf (26)

Homo sapiens (Human) (9)

1a	Arf-1z6yB01	B:5-175
1b	Arf-1z6yB02	B:5-175

Asymmetric Unit(hide GO term definitions)

Chain A,B (ARL5A_HUMAN | Q9Y689)

molecular function
	GO:0005525	GTP binding	Interacting selectively and non-covalently with GTP, guanosine triphosphate.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
	GO:0007264	small GTPase mediated signal transduction	Any series of molecular signals in which a small monomeric GTPase relays one or more of the signals.
cellular component
	GO:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

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Biological Units
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	ARL5A_HUMAN \| Q9Y689	:	1zj6 2h16 2h17

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Description

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Ligands, Modified Residues, Ions (1, 2)

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SS Bonds (0, 0)

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