1S8F - JenaLib

Asymmetric Unit (5, 10)

No.	Name	Count	Type	Full Name
1	BEZ	4	Ligand/Ion	BENZOIC ACID
2	CL	1	Ligand/Ion	CHLORIDE ION
3	GDP	2	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
4	MG	1	Ligand/Ion	MAGNESIUM ION
5	SR	2	Ligand/Ion	STRONTIUM ION

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	BEZ	3	Ligand/Ion	BENZOIC ACID
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	GDP	1	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
4	MG	-1	Ligand/Ion	MAGNESIUM ION
5	SR	-1	Ligand/Ion	STRONTIUM ION

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	BEZ	1	Ligand/Ion	BENZOIC ACID
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	GDP	1	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
4	MG	-1	Ligand/Ion	MAGNESIUM ION
5	SR	-1	Ligand/Ion	STRONTIUM ION

Biological Unit 3 (2, 12)

No.	Name	Count	Type	Full Name
1	BEZ	8	Ligand/Ion	BENZOIC ACID
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	GDP	4	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
4	MG	-1	Ligand/Ion	MAGNESIUM ION
5	SR	-1	Ligand/Ion	STRONTIUM ION

Biological Unit 4 (2, 6)

No.	Name	Count	Type	Full Name
1	BEZ	4	Ligand/Ion	BENZOIC ACID
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	GDP	2	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
4	MG	-1	Ligand/Ion	MAGNESIUM ION
5	SR	-1	Ligand/Ion	STRONTIUM ION

Biological Unit 5 (2, 4)

No.	Name	Count	Type	Full Name
1	BEZ	2	Ligand/Ion	BENZOIC ACID
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	GDP	2	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
4	MG	-1	Ligand/Ion	MAGNESIUM ION
5	SR	-1	Ligand/Ion	STRONTIUM ION

Sites (10, 10)

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	SER A:1021 , BEZ A:1502 , GDP A:3400 , HOH A:9005 , HOH A:9009 , HOH A:9024	BINDING SITE FOR RESIDUE SR A 2401
02	AC2	SOFTWARE	SER B:4021 , GDP B:6400 , HOH B:9007 , HOH B:9015 , HOH B:9019 , HOH B:9033	BINDING SITE FOR RESIDUE MG B 5401
03	AC3	SOFTWARE	PHE B:4069 , ARG B:4070 , SER B:4071	BINDING SITE FOR RESIDUE SR B 2001
04	AC4	SOFTWARE	ARG B:4070 , ARG B:4073 , THR B:4074 , HOH B:9011 , HOH B:9069	BINDING SITE FOR RESIDUE CL B 3001
05	AC5	SOFTWARE	GLY A:1017 , VAL A:1018 , GLY A:1019 , LYS A:1020 , SER A:1021 , SER A:1022 , PHE A:1032 , ASN A:1124 , LYS A:1125 , ASP A:1127 , ILE A:1128 , SER A:1154 , ALA A:1155 , LYS A:1156 , BEZ A:1502 , SR A:2401 , HOH A:9009 , HOH A:9024 , HOH A:9026 , HOH A:9081 , HOH A:9085 , HOH A:9152 , HOH A:9224	BINDING SITE FOR RESIDUE GDP A 3400
06	AC6	SOFTWARE	GLY B:4017 , VAL B:4018 , GLY B:4019 , LYS B:4020 , SER B:4021 , SER B:4022 , PHE B:4032 , ASN B:4124 , LYS B:4125 , ASP B:4127 , SER B:4154 , ALA B:4155 , LYS B:4156 , MG B:5401 , HOH B:9007 , HOH B:9019 , HOH B:9033 , HOH B:9095 , HOH B:9145 , HOH B:9150 , HOH B:9219	BINDING SITE FOR RESIDUE GDP B 6400
07	AC7	SOFTWARE	ARG A:1068 , PHE A:1069 , ARG A:1070 , SER A:1071 , LEU A:1072 , BEZ A:1501 , HOH A:9103 , SER B:4071 , HOH B:9043	BINDING SITE FOR RESIDUE BEZ A 1500
08	AC8	SOFTWARE	PHE A:1055 , ARG A:1068 , BEZ A:1500 , HOH A:9023 , HOH A:9048 , HOH A:9116 , PRO B:4075 , HOH B:9017	BINDING SITE FOR RESIDUE BEZ A 1501
09	AC9	SOFTWARE	HIS A:1038 , THR A:1039 , GLN A:1066 , SR A:2401 , GDP A:3400 , HOH A:9009 , HOH A:9010 , HOH A:9024 , HOH A:9054	BINDING SITE FOR RESIDUE BEZ A 1502
10	BC1	SOFTWARE	THR B:4063 , GLU B:4067 , ARG B:4068 , PHE B:4069 , ARG B:4070 , ARG B:4073 , HOH B:9110	BINDING SITE FOR RESIDUE BEZ B 1503

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (1, 2)

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:168
 aligned with RAB9A_CANLF | P24408 from UniProtKB/Swiss-Prot  Length:201

    Alignment length:170
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174
         RAB9A_CANLF      5 SSLFKVILLGDGGVGKSSLMNRYVTNKFDTQLFHTIGVEFLNKDLEVDGHFVTMQIWDTAGQERFRSLRTPFYRGSDCCLLTFSVDDSQSFQNLSNWKKEFIYYADVKEPESFPFVILGNKIDISERQVSTEEAQAWCRDNGDYPYFETSAKDATNVAAAFEEAVRRVLA  174
               SCOP domains d1s8fa_ A: Rab9a                                                                                                                                                           SCOP domains
               CATH domains 1s8fA00 A:1005-1174 P-loop containing nucleotide triphosphate hydrolases                                                                                                   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.....hhhhhhhhhhhh.......eeeeeeeeeeeeee..eeeeeeeeee..hhhhhhhhhhhh....eeeeeee..hhhhhhhhhhhhhhhhhhhh.--.....eeeeee.........hhhhhhhhhhhh....eee.......hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE RAB  PDB: - UniProt: 3-201                                                                                                                                                 PROSITE
               Transcript 1 Exon 1.1  PDB: A:1005-1174 (gaps) UniProt: 1-202 [INCOMPLETE]                                                                                                              Transcript 1
                1s8f A 1005 SSLFKVILLGDGGVGKSSLMNRYVTNKFDTQLFHTIGVEFLNKDLEVDGHFVTMQIWDTAGQERFRSLRTPFYRGSDCCLLTFSVDDSQSFQNLSNWKKEFIYYADV--PESFPFVILGNKIDISERQVSTEEAQAWCRDNGDYPYFETSAKDATNVAAAFEEAVRRVLA 1174
                                  1014      1024      1034      1044      1054      1064      1074      1084      1094      1104      1114      1124      1134      1144      1154      1164      1174
                                                                                                                                   1111  |                                                            
                                                                                                                                      1114

Chain B from PDB  Type:PROTEIN  Length:173
 aligned with RAB9A_CANLF | P24408 from UniProtKB/Swiss-Prot  Length:201

    Alignment length:175
                              1                                                                                                                                                                            
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168     
         RAB9A_CANLF      - --MAGKSSLFKVILLGDGGVGKSSLMNRYVTNKFDTQLFHTIGVEFLNKDLEVDGHFVTMQIWDTAGQERFRSLRTPFYRGSDCCLLTFSVDDSQSFQNLSNWKKEFIYYADVKEPESFPFVILGNKIDISERQVSTEEAQAWCRDNGDYPYFETSAKDATNVAAAFEEAVRRVL  173
               SCOP domains d1s8fb_ B: Rab9a                                                                                                                                                                SCOP domains
               CATH domains 1s8fB00 B:3999-4173 P-loop containi  ng nucleotide triphosphate hydrolases                                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeee.....hhhhhhhhhhhh...--..eeeeeeeeeeeeee..eeeeeeeeeee....hhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhh...hhhhh.eeeeee.........hhhhhhhhhhhh....eee.......hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----RAB  PDB: B:4003-4173 UniProt: 3-201                                                                                                                                        PROSITE
               Transcript 1 --Exon 1.1  PDB: B:4001-4173 (gaps) UniProt: 1-202 [INCOMPLETE]                                                                                                                 Transcript 1
                1s8f B 3999 GAMAGKSSLFKVILLGDGGVGKSSLMNRYVTNKFD--LFHTIGVEFLNKDLEVDGHFVTMQIWDTAGQERFRSLRTPFYRGSDCCLLTFSVDDSQSFQNLSNWKKEFIYYADVKEPESFPFVILGNKIDISERQVSTEEAQAWCRDNGDYPYFETSAKDATNVAAAFEEAVRRVL 4173
                                  4008      4018      4028    | 4038      4048      4058      4068      4078      4088      4098      4108      4118      4128      4138      4148      4158      4168     
                                                           4033  |                                                                                                                                         
                                                              4036

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 (26, 26)

Asymmetric Unit(hide GO term definitions)

Chain A,B (RAB9A_CANLF | P24408)

molecular function
	GO:0019003	GDP binding	Interacting selectively and non-covalently with GDP, guanosine 5'-diphosphate.
	GO:0005525	GTP binding	Interacting selectively and non-covalently with GTP, guanosine triphosphate.
	GO:0003924	GTPase activity	Catalysis of the reaction: GTP + H2O = GDP + phosphate.
	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.
	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).
biological process
	GO:0052405	negative regulation by host of symbiont molecular function	Any process in which an organism stops, prevents, or reduces the frequency, rate or extent of the functional activity of symbiont proteins. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction.
	GO:0045921	positive regulation of exocytosis	Any process that activates or increases the frequency, rate or extent of exocytosis.
	GO:0015031	protein transport	The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0032880	regulation of protein localization	Any process that modulates the frequency, rate or extent of any process in which a protein is transported to, or maintained in, a specific location.
	GO:0042147	retrograde transport, endosome to Golgi	The directed movement of membrane-bounded vesicles from endosomes back to the trans-Golgi network where they are recycled for further rounds of transport.
	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.
	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:0005794	Golgi apparatus	A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
	GO:0000139	Golgi membrane	The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
	GO:0031410	cytoplasmic vesicle	A vesicle found in the cytoplasm of a cell.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0005783	endoplasmic reticulum	The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
	GO:0005789	endoplasmic reticulum membrane	The lipid bilayer surrounding the endoplasmic reticulum.
	GO:0005768	endosome	A vacuole to which materials ingested by endocytosis are delivered.
	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.
	GO:0005770	late endosome	A prelysosomal endocytic organelle differentiated from early endosomes by lower lumenal pH and different protein composition. Late endosomes are more spherical than early endosomes and are mostly juxtanuclear, being concentrated near the microtubule organizing center.
	GO:0005764	lysosome	A small lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0045335	phagocytic vesicle	A membrane-bounded intracellular vesicle that arises from the ingestion of particulate material by phagocytosis.
	GO:0030670	phagocytic vesicle membrane	The lipid bilayer surrounding a phagocytic vesicle.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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		Biological Unit 5	[ Jena3D ]

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	1s8f
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	RAB9A_CANLF \| P24408
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 10)