1Z0D - JenaLib

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:30 , LYS A:34 , ALA A:78 , GLY A:79 , LEU A:80 , GLU A:81 , HOH A:702 , HOH A:703 , HOH A:704 , HOH A:706 , HOH A:760 , ASN C:172	BINDING SITE FOR RESIDUE PO4 A 600
2	AC2	SOFTWARE	SER A:35 , GDP A:700 , HOH A:706 , HOH A:709 , HOH A:718 , HOH A:724	BINDING SITE FOR RESIDUE MG A 601
3	AC3	SOFTWARE	SER C:35 , GDP C:900 , HOH C:907 , HOH C:913 , HOH C:916 , HOH C:923	BINDING SITE FOR RESIDUE MG C 800
4	AC4	SOFTWARE	ALA A:31 , VAL A:32 , GLY A:33 , LYS A:34 , SER A:35 , SER A:36 , PHE A:46 , HIS A:47 , GLU A:48 , GLN A:50 , ASN A:134 , LYS A:135 , ASP A:137 , LEU A:138 , SER A:164 , ALA A:165 , LYS A:166 , MG A:601 , HOH A:706 , HOH A:708 , HOH A:716 , HOH A:718 , HOH A:736 , HOH A:752 , THR C:167	BINDING SITE FOR RESIDUE GDP A 700
5	AC5	SOFTWARE	ALA C:31 , VAL C:32 , GLY C:33 , LYS C:34 , SER C:35 , SER C:36 , PHE C:46 , GLU C:48 , ASN C:134 , LYS C:135 , ASP C:137 , LEU C:138 , SER C:164 , ALA C:165 , LYS C:166 , MG C:800 , HOH C:907 , HOH C:916 , HOH C:923 , HOH C:933 , HOH C:945 , HOH C:984	BINDING SITE FOR RESIDUE GDP C 900

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

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:165
 aligned with RAB5C_MOUSE | P35278 from UniProtKB/Swiss-Prot  Length:216

    Alignment length:165
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178     
          RAB5C_MOUSE    19 ICQFKLVLLGESAVGKSSLVLRFVKGQFHEYQESTIGAAFLTQTVCLDDTTVKFEIWDTAGQERYHSLAPMYYRGAQAAIVVYDITNTDTFARAKNWVKELQRQASPNIVIALAGNKADLASKRAVEFQEAQAYADDNSLLFMETSAKTAMNVNEIFMAIAKKLP 183
               SCOP domains d1z0da1 A:19-183 Rab5c                                                                                                                                                SCOP domains
               CATH domains 1z0dA00 A:19-183 P-loop containing nucleotide triphosphate hydrolases                                                                                                 CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.....hhhhhhhhhhhh..........eeeeeeeeeee..eeeeeeeeeee....hhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhh....eeeeeeehhhhhhhh..hhhhhhhhhhhh..eeee.......hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1z0d A  19 ICQFKLVLLGESAVGKSSLVLRFVKGQFHEYQESTIGAAFLTQTVCLDDTTVKFEIWDTAGLERYHSLAPMYYRGAQAAIVVYDITNTDTFARAKNWVKELQRQASPNIVIALAGNKADLASKRAVEFQEAQAYADDNSLLFMETSAKTAMNVNEIFMAIAKKLP 183
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178

Chain C from PDB  Type:PROTEIN  Length:165
 aligned with RAB5C_MOUSE | P35278 from UniProtKB/Swiss-Prot  Length:216

    Alignment length:165
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178     
          RAB5C_MOUSE    19 ICQFKLVLLGESAVGKSSLVLRFVKGQFHEYQESTIGAAFLTQTVCLDDTTVKFEIWDTAGQERYHSLAPMYYRGAQAAIVVYDITNTDTFARAKNWVKELQRQASPNIVIALAGNKADLASKRAVEFQEAQAYADDNSLLFMETSAKTAMNVNEIFMAIAKKLP 183
               SCOP domains d1z0dc_ C: Rab5c                                                                                                                                                      SCOP domains
               CATH domains 1z0dC00 C:19-183 P-loop containing nucleotide triphosphate hydrolases                                                                                                 CATH domains
           Pfam domains (1) ----Ras-1z0dC01 C:23-183                                                                                                                                              Pfam domains (1)
           Pfam domains (2) ----Ras-1z0dC02 C:23-183                                                                                                                                              Pfam domains (2)
         Sec.struct. author .eeeeeeee.....hhhhhhhhhhhh...........eeeeeeeeee..eeeeeeeeee.hhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhh....eeeeeeehhhhhhhh..hhhhhhhhhhhh..eeee.......hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1z0d C  19 ICQFKLVLLGESAVGKSSLVLRFVKGQFHEYQESTIGAAFLTQTVCLDDTTVKFEIWDTAGLERYHSLAPMYYRGAQAAIVVYDITNTDTFARAKNWVKELQRQASPNIVIALAGNKADLASKRAVEFQEAQAYADDNSLLFMETSAKTAMNVNEIFMAIAKKLP 183
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178

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 (1, 2)

Gene Ontology (22, 22)

Asymmetric Unit(hide GO term definitions)

Chain A,C (RAB5C_MOUSE | P35278)

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:0007032	endosome organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of endosomes.
	GO:0048227	plasma membrane to endosome transport	Transport of a vesicle from the plasma membrane to the endosome.
	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:0030100	regulation of endocytosis	Any process that modulates the frequency, rate or extent of endocytosis.
	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:0005769	early endosome	A membrane-bounded organelle that receives incoming material from primary endocytic vesicles that have been generated by clathrin-dependent and clathrin-independent endocytosis; vesicles fuse with the early endosome to deliver cargo for sorting into recycling or degradation pathways.
	GO:0031901	early endosome membrane	The lipid bilayer surrounding an early endosome.
	GO:0030139	endocytic vesicle	A membrane-bounded intracellular vesicle formed by invagination of the plasma membrane around an extracellular substance. Endocytic vesicles fuse with early endosomes to deliver the cargo for further sorting.
	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:0043231	intracellular membrane-bounded organelle	Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
	GO:0005811	lipid droplet	An intracellular non-membrane-bounded organelle comprising a matrix of coalesced lipids surrounded by a phospholipid monolayer. May include associated proteins.
	GO:0005765	lysosomal membrane	The lipid bilayer surrounding the lysosome and separating its contents from the cell cytoplasm.
	GO:0042470	melanosome	A tissue-specific, membrane-bounded cytoplasmic organelle within which melanin pigments are synthesized and stored. Melanosomes are synthesized in melanocyte cells.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	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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	1z0d
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 5)

Sites (5, 5)