3NKV - JenaLib

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:17 , GLY A:18 , VAL A:19 , GLY A:20 , LYS A:21 , SER A:22 , CYS A:23 , TYR A:33 , THR A:34 , GLU A:35 , SER A:36 , SER A:39 , THR A:40 , GLY A:66 , ASN A:121 , LYS A:122 , ASP A:124 , LEU A:125 , SER A:151 , ALA A:152 , LYS A:153 , HOH A:187 , HOH A:189 , HOH A:191 , HOH A:208 , HOH A:211 , HOH A:218 , HOH A:291 , MG A:500	BINDING SITE FOR RESIDUE GNP A 400
2	AC2	SOFTWARE	SER A:22 , THR A:40 , HOH A:189 , HOH A:218 , GNP A:400	BINDING SITE FOR RESIDUE MG A 500
3	AC3	SOFTWARE	ILE A:41 , VAL A:43 , ASP A:44 , HOH A:261	BINDING SITE FOR RESIDUE BA A 175
4	AC4	SOFTWARE	VAL A:43 , PHE A:45 , GLN A:60 , TRP A:62 , TYR A:77 , HOH A:281	BINDING SITE FOR RESIDUE AMP A 600
5	AC5	SOFTWARE	SER B:17 , GLY B:18 , VAL B:19 , GLY B:20 , LYS B:21 , SER B:22 , CYS B:23 , TYR B:33 , GLU B:35 , THR B:40 , GLY B:66 , ASN B:121 , LYS B:122 , ASP B:124 , LEU B:125 , SER B:151 , ALA B:152 , LYS B:153 , HOH B:181 , HOH B:185 , HOH B:199 , HOH B:204 , HOH B:212 , HOH B:215 , HOH B:227 , HOH B:278 , MG B:500	BINDING SITE FOR RESIDUE GNP B 400
6	AC6	SOFTWARE	SER B:22 , THR B:40 , HOH B:185 , HOH B:199 , GNP B:400	BINDING SITE FOR RESIDUE MG B 500
7	AC7	SOFTWARE	GLU A:4 , ASP A:6 , THR A:56 , ASP B:132 , THR B:134 , HOH B:187 , HOH B:228 , HOH B:301	BINDING SITE FOR RESIDUE BA B 175
8	AC8	SOFTWARE	PHE B:45 , TRP B:62 , TYR B:77 , HOH B:176 , HOH B:216 , HOH B:256	BINDING SITE FOR RESIDUE AMP B 600

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

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:170
 aligned with RAB1B_HUMAN | Q9H0U4 from UniProtKB/Swiss-Prot  Length:201

    Alignment length:170
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173
          RAB1B_HUMAN     4 EYDYLFKLLLIGDSGVGKSCLLLRFADDTYTESYISTIGVDFKIRTIELDGKTIKLQIWDTAGQERFRTITSSYYRGAHGIIVVYDVTDQESYANVKQWLQEIDRYASENVNKLLVGNKSDLTTKKVVDNTTAKEFADSLGIPFLETSAKNATNVEQAFMTMAAEIKKRM 173
               SCOP domains d3nkva_ A: automated matches                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee....hhhhhhhhhhhh...........eeeeeeeeee..eeeeeeeeee..hhhhhhhhhh......eeeeeee..hhhhhhhhhhhhhhhhhhh....eeeeeee..........hhhhhhhhhhhh...eee.......hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE RAB  PDB: A:4-173 UniProt: 4-201                                                                                                                                           PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nkv A   4 EYDYLFKLLLIGDSGVGKSCLLLRFADDTYTESYISTIGVDFKIRTIELDGKTIKLQIWDTAGQERFRTITSSYYRGAHGIIVVYDVTDQESYANVKQWLQEIDRYASENVNKLLVGNKSDLTTKKVVDNTTAKEFADSLGIPFLETSAKNATNVEQAFMTMAAEIKKRM 173
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173

Chain B from PDB  Type:PROTEIN  Length:169
 aligned with RAB1B_HUMAN | Q9H0U4 from UniProtKB/Swiss-Prot  Length:201

    Alignment length:170
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173
          RAB1B_HUMAN     4 EYDYLFKLLLIGDSGVGKSCLLLRFADDTYTESYISTIGVDFKIRTIELDGKTIKLQIWDTAGQERFRTITSSYYRGAHGIIVVYDVTDQESYANVKQWLQEIDRYASENVNKLLVGNKSDLTTKKVVDNTTAKEFADSLGIPFLETSAKNATNVEQAFMTMAAEIKKRM 173
               SCOP domains d3nkvb_ B: automated matches                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------Ras-3nkvB01 B:10-171                                                                                                                                              -- Pfam domains (1)
           Pfam domains (2) ------Ras-3nkvB02 B:10-171                                                                                                                                              -- Pfam domains (2)
         Sec.struct. author ...eeeeeeeee....hhhhhhhhhhhh...........eeeeeeeeee..eeeeeeeeee..hhhhhhhhhh......eeeeeee..hhhhhhhhhhhhhhhhhhh.-..eeeeeee...hhhhh..hhhhhhhhhhhh...eeee......hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE RAB  PDB: B:4-173 UniProt: 4-201                                                                                                                                           PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nkv B   4 EYDYLFKLLLIGDSGVGKSCLLLRFADDTYTESYISTIGVDFKIRTIELDGKTIKLQIWDTAGQERFRTITSSYYRGAHGIIVVYDVTDQESYANVKQWLQEIDRYAS-NVNKLLVGNKSDLTTKKVVDNTTAKEFADSLGIPFLETSAKNATNVEQAFMTMAAEIKKRM 173
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173
                                                                                                                                     111 |                                                            
                                                                                                                                       113

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 (0, 0)

Pfam Domains (1, 2)

Gene Ontology (25, 25)

Asymmetric Unit(hide GO term definitions)

Chain A,B (RAB1B_HUMAN | Q9H0U4)

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.
	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:0048208	COPII vesicle coating	The addition of COPII proteins and adaptor proteins to ER membranes during the formation of transport vesicles, forming a vesicle coat.
	GO:0006888	ER to Golgi vesicle-mediated transport	The directed movement of substances from the endoplasmic reticulum (ER) to the Golgi, mediated by COP II vesicles. Small COP II coated vesicles form from the ER and then fuse directly with the cis-Golgi. Larger structures are transported along microtubules to the cis-Golgi.
	GO:0006914	autophagy	The process in which cells digest parts of their own cytoplasm; allows for both recycling of macromolecular constituents under conditions of cellular stress and remodeling the intracellular structure for cell differentiation.
	GO:0090557	establishment of endothelial intestinal barrier	The establishment of a barrier between endothelial cell layers of the intestine to exert specific and selective control over the passage of water and solutes, thus allowing formation and maintenance of compartments that differ in fluid and solute composition.
	GO:1903020	positive regulation of glycoprotein metabolic process	Any process that activates or increases the frequency, rate or extent of glycoprotein metabolic process.
	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:2000785	regulation of autophagosome assembly	Any process that modulates the frequency, rate or extent of autophagosome assembly.
	GO:0006890	retrograde vesicle-mediated transport, Golgi to ER	The directed movement of substances from the Golgi back to the endoplasmic reticulum, mediated by vesicles bearing specific protein coats such as COPI or COG.
	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.
	GO:0019068	virion assembly	A late phase of the viral life cycle during which all the components necessary for the formation of a mature virion collect at a particular site in the cell and the basic structure of the virus particle is formed.
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:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005789	endoplasmic reticulum membrane	The lipid bilayer surrounding the endoplasmic reticulum.
	GO:0005793	endoplasmic reticulum-Golgi intermediate compartment	A complex system of membrane-bounded compartments located between endoplasmic reticulum (ER) and the Golgi complex, with a distinctive membrane protein composition; involved in ER-to-Golgi and Golgi-to-ER transport.
	GO:0033116	endoplasmic reticulum-Golgi intermediate compartment membrane	The lipid bilayer surrounding any of the compartments of the endoplasmic reticulum (ER)-Golgi intermediate compartment system.
	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:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
	GO:0034045	pre-autophagosomal structure membrane	A cellular membrane associated with the pre-autophagosomal structure.
	GO:0030133	transport vesicle	Any of the vesicles of the constitutive secretory pathway, which carry cargo from the endoplasmic reticulum to the Golgi, between Golgi cisternae, from the Golgi to the ER (retrograde transport) or to destinations within or outside the cell.

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 8)

Sites (8, 8)