1TU3 - JenaLib

Asym.Unit - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF RAB5 COMPLEX WITH RABAPTIN5 C-TERMINAL DOMAIN

Authors :   G. Zhu, P. Zhai, J. Liu, S. Terzyan, G. Li, X. C. Zhang

Date :   24 Jun 04 (Deposition) - 05 Oct 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.31

Chains :   Asym. Unit : A,B,C,D,E,F,G,H,I,J
Biol. Unit 1: A,B,F,G  (1x)
Biol. Unit 2: C,D,H,I  (1x)
Biol. Unit 3: E,J  (2x)

Keywords :   Rab5, Rabaptin5, Effector-Binding, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. Zhu, P. Zhai, J. Liu, S. Terzyan, G. Li, X. C. Zhang
Structural Basis Of Rab5-Rabaptin5 Interaction In Endocytosis
Nat. Struct. Mol. Biol. V. 11 975 2004
PubMed-ID: 15378032 | Reference-DOI: 10.1038/NSMB832
(for further references see the PDB file header)

Molecule 1 - RAS-RELATED PROTEIN RAB-5A
	Chains	:	A, B, C, D, E
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET11A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	RAB5A, RAB5
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 2 - RAB GTPASE BINDING EFFECTOR PROTEIN 1
	Chains	:	F, G, H, I, J
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PGEX6P-1
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	RABEP1, RABPT5, RABPT5A
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	RABAPTIN-5, RABAPTIN-5ALPHA, RABAPTIN-4

		1	2	3	4	5	6	7	8	9	10
Asymmetric Unit	:	A	B	C	D	E	F	G	H	I	J
Biological Unit 1 (1x)	:	A	B				F	G
Biological Unit 2 (1x)	:			C	D				H	I
Biological Unit 3 (2x)	:					E					J

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 10)

No.	Name	Count	Type	Full Name
1	GNP	5	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2	MG	5	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (1, 2)

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

Biological Unit 2 (1, 2)

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

Biological Unit 3 (1, 2)

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

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	SER A:34 , THR A:52 , HOH A:404 , HOH A:405 , GNP A:1202	BINDING SITE FOR RESIDUE MG A 1201
02	AC2	SOFTWARE	SER B:34 , THR B:52 , HOH B:420 , HOH B:421 , GNP B:2202	BINDING SITE FOR RESIDUE MG B 2201
03	AC3	SOFTWARE	SER C:34 , THR C:52 , HOH C:431 , HOH C:432 , GNP C:3202	BINDING SITE FOR RESIDUE MG C 3201
04	AC4	SOFTWARE	SER D:34 , THR D:52 , HOH D:440 , HOH D:441 , GNP D:4202	BINDING SITE FOR RESIDUE MG D 4201
05	AC5	SOFTWARE	SER E:34 , THR E:52 , HOH E:450 , HOH E:451 , GNP E:5202	BINDING SITE FOR RESIDUE MG E 5201
06	AC6	SOFTWARE	SER A:29 , ALA A:30 , VAL A:31 , GLY A:32 , LYS A:33 , SER A:34 , SER A:35 , PHE A:45 , HIS A:46 , GLU A:47 , GLN A:49 , GLU A:50 , SER A:51 , THR A:52 , GLY A:78 , ASN A:133 , LYS A:134 , ASP A:136 , LEU A:137 , SER A:163 , ALA A:164 , LYS A:165 , HOH A:403 , HOH A:404 , HOH A:405 , HOH A:592 , MG A:1201	BINDING SITE FOR RESIDUE GNP A 1202
07	AC7	SOFTWARE	SER B:29 , ALA B:30 , VAL B:31 , GLY B:32 , LYS B:33 , SER B:34 , SER B:35 , PHE B:45 , HIS B:46 , GLU B:47 , GLN B:49 , SER B:51 , THR B:52 , GLY B:78 , ASN B:133 , LYS B:134 , ASP B:136 , LEU B:137 , SER B:163 , ALA B:164 , LYS B:165 , HOH B:420 , HOH B:421 , MG B:2201	BINDING SITE FOR RESIDUE GNP B 2202
08	AC8	SOFTWARE	SER C:29 , ALA C:30 , VAL C:31 , GLY C:32 , LYS C:33 , SER C:34 , SER C:35 , PHE C:45 , HIS C:46 , GLU C:47 , GLN C:49 , SER C:51 , THR C:52 , GLY C:78 , ASN C:133 , LYS C:134 , ASP C:136 , SER C:163 , ALA C:164 , LYS C:165 , HOH C:431 , HOH C:432 , MG C:3201	BINDING SITE FOR RESIDUE GNP C 3202
09	AC9	SOFTWARE	SER D:29 , ALA D:30 , VAL D:31 , GLY D:32 , LYS D:33 , SER D:34 , SER D:35 , PHE D:45 , GLN D:49 , GLU D:50 , SER D:51 , THR D:52 , GLY D:78 , ASN D:133 , LYS D:134 , ASP D:136 , LEU D:137 , SER D:163 , ALA D:164 , LYS D:165 , HOH D:440 , HOH D:441 , HOH D:442 , MG D:4201	BINDING SITE FOR RESIDUE GNP D 4202
10	BC1	SOFTWARE	SER E:29 , ALA E:30 , VAL E:31 , GLY E:32 , LYS E:33 , SER E:34 , SER E:35 , PHE E:45 , HIS E:46 , GLU E:47 , GLN E:49 , SER E:51 , THR E:52 , GLY E:78 , ASN E:133 , LYS E:134 , ASP E:136 , LEU E:137 , SER E:163 , ALA E:164 , LYS E:165 , HOH E:450 , HOH E:451 , HOH E:454 , MG E:5201	BINDING SITE FOR RESIDUE GNP E 5202

(no "SS Bond" information available for 1TU3)

(no "Cis Peptide Bond" information available for 1TU3)

(no "SAP(SNP)/Variant" information available for 1TU3)

(no "PROSITE Motif" information available for 1TU3)

Asymmetric Unit (5, 25)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000273047	1a	ENSE00001769725	chr3:19988571-19989013	443	RAB5A_HUMAN	-	0	0	-	-
1.2b	ENST00000273047	2b	ENSE00001162720	chr3:19992298-19992553	256	RAB5A_HUMAN	1-55	55	5	A:18-55 B:17-55 C:19-55 D:22-55 (gaps) E:16-55	38 39 37 34 40
1.4c	ENST00000273047	4c	ENSE00001691424	chr3:20017093-20017244	152	RAB5A_HUMAN	55-105	51	5	A:55-105 B:55-105 C:55-105 D:55-105 (gaps) E:55-105	51 51 51 51 51
1.5b	ENST00000273047	5b	ENSE00001783762	chr3:20017539-20017661	123	RAB5A_HUMAN	106-146	41	5	A:106-146 B:106-146 C:106-146 D:106-146 (gaps) E:106-146	41 41 41 41 41
1.6a	ENST00000273047	6a	ENSE00001688303	chr3:20019802-20019895	94	RAB5A_HUMAN	147-178	32	5	A:147-178 B:147-178 C:147-178 D:147-178 E:147-178	32 32 32 32 32
1.7e	ENST00000273047	7e	ENSE00001368096	chr3:20025200-20026667	1468	RAB5A_HUMAN	178-215	38	5	A:178-182 B:178-182 C:178-184 D:178-182 E:178-182	5 5 7 5 5

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 RAB5A_HUMAN | P20339 from UniProtKB/Swiss-Prot  Length:215

    Alignment length:165
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177     
          RAB5A_HUMAN    18 ICQFKLVLLGESAVGKSSLVLRFVKGQFHEFQESTIGAAFLTQTVCLDDTTVKFEIWDTAGQERYHSLAPMYYRGAQAAIVVYDITNEESFARAKNWVKELQRQASPNIVIALSGNKADLANKRAVDFQEAQSYADDNSLLFMETSAKTSMNVNEIFMAIAKKLP 182
               SCOP domains d1tu3a_ A: Rab5a                                                                                                                                                      SCOP domains
               CATH domains 1tu3A00 A:18-182 P-loop containing nucleotide triphosphate hydrolases                                                                                                 CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.....hhhhhhhhhhhh...........eeeeeeeee....eeeeeeeee..hhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhh....eeeeeeehhhhhhhh..hhhhhhhhhhhh..eeee.......hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2b  PDB: A:18-55 UniProt: 1-55 --------------------------------------------------Exon 1.5b  PDB: A:106-146                Exon 1.6a  PDB: A:147-178       ---- Transcript 1 (1)
           Transcript 1 (2) -------------------------------------Exon 1.4c  PDB: A:55-105 UniProt: 55-105           ------------------------------------------------------------------------1.7e  Transcript 1 (2)
                 1tu3 A  18 ICQFKLVLLGESAVGKSSLVLRFVKGQFHEFQESTIGAAFLTQTVCLDDTTVKFEIWDTAGQERYHSLAPMYYRGAQAAIVVYDITNEESFARAKNWVKELQRQASPNIVIALSGNKADLANKRAVDFQEAQSYADDNSLLFMETSAKTSMNVNEIFMAIAKKLP 182
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177

Chain B from PDB  Type:PROTEIN  Length:166
 aligned with RAB5A_HUMAN | P20339 from UniProtKB/Swiss-Prot  Length:215

    Alignment length:166
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176      
          RAB5A_HUMAN    17 KICQFKLVLLGESAVGKSSLVLRFVKGQFHEFQESTIGAAFLTQTVCLDDTTVKFEIWDTAGQERYHSLAPMYYRGAQAAIVVYDITNEESFARAKNWVKELQRQASPNIVIALSGNKADLANKRAVDFQEAQSYADDNSLLFMETSAKTSMNVNEIFMAIAKKLP 182
               SCOP domains d1tu3b_ B: Rab5a                                                                                                                                                       SCOP domains
               CATH domains 1tu3B00 B:17-182 P-loop containing nucleotide triphosphate hydrolases                                                                                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee.....hhhhhhhhhhhh...........eeeeeeeee....eeeeeeeee..hhhhhhhhhhhhh...eeeeeee...hhhhhhhhhhhhhhhhhh....eeeeeee.hhhhhhh..hhhhhhhhhhhh..eeeee......hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2b  PDB: B:17-55 UniProt: 1-55  --------------------------------------------------Exon 1.5b  PDB: B:106-146                Exon 1.6a  PDB: B:147-178       ---- Transcript 1 (1)
           Transcript 1 (2) --------------------------------------Exon 1.4c  PDB: B:55-105 UniProt: 55-105           ------------------------------------------------------------------------1.7e  Transcript 1 (2)
                 1tu3 B  17 KICQFKLVLLGESAVGKSSLVLRFVKGQFHEFQESTIGAAFLTQTVCLDDTTVKFEIWDTAGQERYHSLAPMYYRGAQAAIVVYDITNEESFARAKNWVKELQRQASPNIVIALSGNKADLANKRAVDFQEAQSYADDNSLLFMETSAKTSMNVNEIFMAIAKKLP 182
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176

Chain C from PDB  Type:PROTEIN  Length:166
 aligned with RAB5A_HUMAN | P20339 from UniProtKB/Swiss-Prot  Length:215

    Alignment length:166
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178      
          RAB5A_HUMAN    19 CQFKLVLLGESAVGKSSLVLRFVKGQFHEFQESTIGAAFLTQTVCLDDTTVKFEIWDTAGQERYHSLAPMYYRGAQAAIVVYDITNEESFARAKNWVKELQRQASPNIVIALSGNKADLANKRAVDFQEAQSYADDNSLLFMETSAKTSMNVNEIFMAIAKKLPKN 184
               SCOP domains d1tu3c_ C: Rab5a                                                                                                                                                       SCOP domains
               CATH domains 1tu3C00 C:19-184 P-loop containing nucleotide triphosphate hydrolases                                                                                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhhh............eeee..eee....eeeeeeeee..hhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhh....eeeeeee..........hhhhhhhhhhhh....ee.......hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2b  PDB: C:19-55 UniProt: 1-55--------------------------------------------------Exon 1.5b  PDB: C:106-146                Exon 1.6a  PDB: C:147-178       ------ Transcript 1 (1)
           Transcript 1 (2) ------------------------------------Exon 1.4c  PDB: C:55-105 UniProt: 55-105           ------------------------------------------------------------------------1.7e    Transcript 1 (2)
                 1tu3 C  19 CQFKLVLLGESAVGKSSLVLRFVKGQFHEFQESTIGAAFLTQTVCLDDTTVKFEIWDTAGQERYHSLAPMYYRGAQAAIVVYDITNEESFARAKNWVKELQRQASPNIVIALSGNKADLANKRAVDFQEAQSYADDNSLLFMETSAKTSMNVNEIFMAIAKKLPKN 184
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178

Chain D from PDB  Type:PROTEIN  Length:147
 aligned with RAB5A_HUMAN | P20339 from UniProtKB/Swiss-Prot  Length:215

    Alignment length:161
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181 
          RAB5A_HUMAN    22 KLVLLGESAVGKSSLVLRFVKGQFHEFQESTIGAAFLTQTVCLDDTTVKFEIWDTAGQERYHSLAPMYYRGAQAAIVVYDITNEESFARAKNWVKELQRQASPNIVIALSGNKADLANKRAVDFQEAQSYADDNSLLFMETSAKTSMNVNEIFMAIAKKLP 182
               SCOP domains d1tu3d_ D: Rab5a                                                                                                                                                  SCOP domains
               CATH domains 1tu3D00 D:22-182 P-loop    containing nucl  eoti  de triphosphate hydrolases                                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.....hhhhhhhhhhh...---......eeee.....--....--.eeee..hhhhhhhhhhh.....eeeeeee..hhhhhhhhhhhhhhh-------.eeeeeee..........hhhhhhhhhhhh.............hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2b  PDB: D:22-55 (gaps)    --------------------------------------------------Exon 1.5b  PDB: D:106-146 (gaps)         Exon 1.6a  PDB: D:147-178       ---- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------Exon 1.4c  PDB: D:55-105 (gaps) UniProt: 55-105    ------------------------------------------------------------------------1.7e  Transcript 1 (2)
                 1tu3 D  22 KLVLLGESAVGKSSLVLRFVKGQF---QESTIGAAFLTQTVC--DTTV--EIWDTAGQERYHSLAPMYYRGAQAAIVVYDITNEESFARAKNWVKEL-------IVIALSGNKADLANKRAVDFQEAQSYADDNSLLFMETSAKTSMNVNEIFMAIAKKLP 182
                                    31        41   |   |51        61 |  |  | -|       81        91       101       111      |  -    |  131       141       151       161       171       181 
                                                  45  49            63 66 69 72                                           118     126

Chain E from PDB  Type:PROTEIN  Length:167
 aligned with RAB5A_HUMAN | P20339 from UniProtKB/Swiss-Prot  Length:215

    Alignment length:167
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       
          RAB5A_HUMAN    16 NKICQFKLVLLGESAVGKSSLVLRFVKGQFHEFQESTIGAAFLTQTVCLDDTTVKFEIWDTAGQERYHSLAPMYYRGAQAAIVVYDITNEESFARAKNWVKELQRQASPNIVIALSGNKADLANKRAVDFQEAQSYADDNSLLFMETSAKTSMNVNEIFMAIAKKLP 182
               SCOP domains d1tu3e_ E: Rab5a                                                                                                                                                        SCOP domains
               CATH domains 1tu3E00 E:16-182 P-loop containing nucleotide triphosphate hydrolases                                                                                                   CATH domains
           Pfam domains (1) ------Ras-1tu3E01 E:22-182                                                                                                                                              Pfam domains (1)
           Pfam domains (2) ------Ras-1tu3E02 E:22-182                                                                                                                                              Pfam domains (2)
           Pfam domains (3) ------Ras-1tu3E03 E:22-182                                                                                                                                              Pfam domains (3)
           Pfam domains (4) ------Ras-1tu3E04 E:22-182                                                                                                                                              Pfam domains (4)
           Pfam domains (5) ------Ras-1tu3E05 E:22-182                                                                                                                                              Pfam domains (5)
         Sec.struct. author ..eeeeeeeee.....hhhhhhhhhhhh...........eeeeeeeee....eeeeeeeee..hhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhh....eeeeeeehhhhh.....hhhhhhhhhhhh..eeee.......hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2b  PDB: E:16-55 UniProt: 1-55   --------------------------------------------------Exon 1.5b  PDB: E:106-146                Exon 1.6a  PDB: E:147-178       ---- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------Exon 1.4c  PDB: E:55-105 UniProt: 55-105           ------------------------------------------------------------------------1.7e  Transcript 1 (2)
                 1tu3 E  16 NKICQFKLVLLGESAVGKSSLVLRFVKGQFHEFQESTIGAAFLTQTVCLDDTTVKFEIWDTAGQERYHSLAPMYYRGAQAAIVVYDITNEESFARAKNWVKELQRQASPNIVIALSGNKADLANKRAVDFQEAQSYADDNSLLFMETSAKTSMNVNEIFMAIAKKLP 182
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175

Chain F from PDB  Type:PROTEIN  Length:46
 aligned with RABE1_HUMAN | Q15276 from UniProtKB/Swiss-Prot  Length:862

    Alignment length:46
                                   813       823       833       843      
          RABE1_HUMAN   804 AQRLQTELDVSEQVQRDFVKLSQTLQVQLERIRQADSLERIRAILN 849
               SCOP domains d1tu3f_ F: Rabaptin-5                          SCOP domains
               CATH domains ---------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------- PROSITE
                 Transcript ---------------------------------------------- Transcript
                 1tu3 F 804 AQRLQTELDVSEQVQRDFVKLSQTLQVQLERIRQADSLERIRAILN 849
                                   813       823       833       843

Chain G from PDB  Type:PROTEIN  Length:51
 aligned with RABE1_HUMAN | Q15276 from UniProtKB/Swiss-Prot  Length:862

    Alignment length:51
                                   811       821       831       841       851 
          RABE1_HUMAN   802 NKAQRLQTELDVSEQVQRDFVKLSQTLQVQLERIRQADSLERIRAILNDTK 852
               SCOP domains d1tu3g_ G: Rabaptin-5                               SCOP domains
               CATH domains --------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------- Transcript
                 1tu3 G 802 NKAQRLQTELDVSEQVQRDFVKLSQTLQVQLERIRQADSLERIRAILNDTK 852
                                   811       821       831       841       851

Chain H from PDB  Type:PROTEIN  Length:44
 aligned with RABE1_HUMAN | Q15276 from UniProtKB/Swiss-Prot  Length:862

    Alignment length:44
                                   815       825       835       845    
          RABE1_HUMAN   806 RLQTELDVSEQVQRDFVKLSQTLQVQLERIRQADSLERIRAILN 849
               SCOP domains d1tu3h_ H: Rabaptin-5                        SCOP domains
               CATH domains -------------------------------------------- CATH domains
               Pfam domains -------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------- PROSITE
                 Transcript -------------------------------------------- Transcript
                 1tu3 H 806 RLQTELDVSEQVQRDFVKLSQTLQVQLERIRQADSLERIRAILN 849
                                   815       825       835       845

Chain I from PDB  Type:PROTEIN  Length:45
 aligned with RABE1_HUMAN | Q15276 from UniProtKB/Swiss-Prot  Length:862

    Alignment length:47
                                   813       823       833       843       
          RABE1_HUMAN   804 AQRLQTELDVSEQVQRDFVKLSQTLQVQLERIRQADSLERIRAILND 850
               SCOP domains d1tu3i_ I: Rabaptin-5                           SCOP domains
               CATH domains ----------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..--hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------- PROSITE
                 Transcript ----------------------------------------------- Transcript
                 1tu3 I 804 AQRLQTELDVSEQVQRDFVKLSQTLQVQLERIRQA--LERIRAILND 850
                                   813       823       833    |  843       
                                                            838  |         
                                                               841

Chain J from PDB  Type:PROTEIN  Length:53
 aligned with RABE1_HUMAN | Q15276 from UniProtKB/Swiss-Prot  Length:862

    Alignment length:53
                                   811       821       831       841       851   
          RABE1_HUMAN   802 NKAQRLQTELDVSEQVQRDFVKLSQTLQVQLERIRQADSLERIRAILNDTKLT 854
               SCOP domains d1tu3j_ J: Rabaptin-5                                 SCOP domains
               CATH domains ----------------------------------------------------- CATH domains
           Pfam domains (1) Rab5-b----------------------------------------------- Pfam domains (1)
           Pfam domains (2) Rab5-b----------------------------------------------- Pfam domains (2)
           Pfam domains (3) Rab5-b----------------------------------------------- Pfam domains (3)
           Pfam domains (4) Rab5-b----------------------------------------------- Pfam domains (4)
           Pfam domains (5) Rab5-b----------------------------------------------- Pfam domains (5)
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------- Transcript
                 1tu3 J 802 NKAQRLQTELDVSEQVQRDFVKLSQTLQVQLERIRQADSLERIRAILNDTKLT 854
                                   811       821       831       841       851

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: Rab5a (12)

Human (Homo sapiens) [TaxId: 9606] (12)

1a	d1tu3a_	A:
1b	d1tu3b_	B:
1c	d1tu3c_	C:
1d	d1tu3d_	D:
1e	d1tu3e_	E:

Class: Coiled coil proteins (689)

Fold: Parallel coiled-coil (407)

Superfamily: G protein-binding domain (4)

Family: Rabaptin-5 (2)

Protein domain: Rabaptin-5 (2)

Human (Homo sapiens) [TaxId: 9606] (2)

2a	d1tu3f_	F:
2b	d1tu3g_	G:
2c	d1tu3h_	H:
2d	d1tu3i_	I:
2e	d1tu3j_	J:

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	1tu3E00	E:16-182
1b	1tu3B00	B:17-182
1c	1tu3C00	C:19-184
1d	1tu3A00	A:18-182
1e	1tu3D00	D:22-182

Asymmetric Unit

Clans(

)

Families(

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Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: Ras (176)

Homo sapiens (Human) (141)

1a	Ras-1tu3E01	E:22-182
1b	Ras-1tu3E02	E:22-182
1c	Ras-1tu3E03	E:22-182
1d	Ras-1tu3E04	E:22-182
1e	Ras-1tu3E05	E:22-182

Clan: TPR (230)

Family: Rab5-bind (3)

Homo sapiens (Human) (3)

2a	Rab5-bind-1tu3J01	J:802-807
2b	Rab5-bind-1tu3J02	J:802-807
2c	Rab5-bind-1tu3J03	J:802-807
2d	Rab5-bind-1tu3J04	J:802-807
2e	Rab5-bind-1tu3J05	J:802-807

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E (RAB5A_HUMAN | P20339)

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:0019001	guanyl nucleotide binding	Interacting selectively and non-covalently with guanyl nucleotides, any compound consisting of guanosine esterified with (ortho)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:0007596	blood coagulation	The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers.
	GO:0045022	early endosome to late endosome transport	The directed movement of substances, in membrane-bounded vesicles, from the early sorting endosomes to the late sorting endosomes; transport occurs along microtubules and can be experimentally blocked with microtubule-depolymerizing drugs.
	GO:0006897	endocytosis	A vesicle-mediated transport process in which cells take up external materials or membrane constituents by the invagination of a small region of the plasma membrane to form a new membrane-bounded vesicle.
	GO:0006909	phagocytosis	An endocytosis process that results in the engulfment of external particulate material by phagocytes. The particles are initially contained within phagocytic vacuoles (phagosomes), which then fuse with primary lysosomes to effect digestion of the particles.
	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:2000286	receptor internalization involved in canonical Wnt signaling pathway	A receptor internalization process that contributes to canonical Wnt signaling pathway.
	GO:2000785	regulation of autophagosome assembly	Any process that modulates the frequency, rate or extent of autophagosome assembly.
	GO:0030100	regulation of endocytosis	Any process that modulates the frequency, rate or extent of endocytosis.
	GO:0051036	regulation of endosome size	Any process that modulates the volume of an endosome, a membrane-bounded organelle that carries materials newly ingested by endocytosis.
	GO:0051489	regulation of filopodium assembly	Any process that modulates the frequency, rate or extent of the assembly of a filopodium, a thin, stiff protrusion extended by the leading edge of a motile cell such as a crawling fibroblast or amoeba, or an axonal growth cone.
	GO:2000300	regulation of synaptic vesicle exocytosis	Any process that modulates the frequency, rate or extent of synaptic vesicle exocytosis.
	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:0036465	synaptic vesicle recycling	The trafficking of synaptic vesicles from the pre-synaptic membrane so the vesicle can dock and prime for another round of exocytosis and neurotransmitter release. Recycling occurs after synaptic vesicle exocytosis, and is necessary to replenish presynaptic vesicle pools, sustain transmitter release and preserve the structural integrity of the presynaptic membrane. Recycling can occur following transient fusion with the presynaptic membrane (kiss and run), or via endocytosis of presynaptic membrane.
	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:0015629	actin cytoskeleton	The part of the cytoskeleton (the internal framework of a cell) composed of actin and associated proteins. Includes actin cytoskeleton-associated complexes.
	GO:0030424	axon	The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter.
	GO:0043679	axon terminus	Terminal inflated portion of the axon, containing the specialized apparatus necessary to release neurotransmitters. The axon terminus is considered to be the whole region of thickening and the terminal button is a specialized region of it.
	GO:0042995	cell projection	A prolongation or process extending from a cell, e.g. a flagellum or axon.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0098559	cytoplasmic side of early endosome membrane	The side (leaflet) of the early endosome membrane that faces the cytoplasm.
	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:0030425	dendrite	A neuron projection that has a short, tapering, often branched, morphology, receives and integrates signals from other neurons or from sensory stimuli, and conducts a nerve impulse towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body.
	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:0010008	endosome membrane	The lipid bilayer surrounding an endosome.
	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: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:0045121	membrane raft	Any of the small (10-200 nm), heterogeneous, highly dynamic, sterol- and sphingolipid-enriched membrane domains that compartmentalize cellular processes. Small rafts can sometimes be stabilized to form larger platforms through protein-protein and protein-lipid interactions.
	GO:0043025	neuronal cell body	The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
	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.
	GO:0001726	ruffle	Projection at the leading edge of a crawling cell; the protrusions are supported by a microfilament meshwork.
	GO:0036477	somatodendritic compartment	The region of a neuron that includes the cell body (cell soma) and the dendrite, but excludes the axon.
	GO:0008021	synaptic vesicle	A secretory organelle, typically 50 nm in diameter, of presynaptic nerve terminals; accumulates in high concentrations of neurotransmitters and secretes these into the synaptic cleft by fusion with the 'active zone' of the presynaptic plasma membrane.
	GO:0043195	terminal bouton	Terminal inflated portion of the axon, containing the specialized apparatus necessary to release neurotransmitters. The axon terminus is considered to be the whole region of thickening and the terminal bouton is a specialized region of it.

Chain F,G,H,I,J (RABE1_HUMAN | Q15276)

molecular function
	GO:0005096	GTPase activator activity	Binds to and increases the activity of a GTPase, an enzyme that catalyzes the hydrolysis of GTP.
	GO:0008083	growth factor activity	The function that stimulates a cell to grow or proliferate. Most growth factors have other actions besides the induction of cell growth or proliferation.
	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).
	GO:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
	GO:0006915	apoptotic process	A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
	GO:0006897	endocytosis	A vesicle-mediated transport process in which cells take up external materials or membrane constituents by the invagination of a small region of the plasma membrane to form a new membrane-bounded vesicle.
	GO:0061025	membrane fusion	The membrane organization process that joins two lipid bilayers to form a single membrane.
	GO:0043547	positive regulation of GTPase activity	Any process that activates or increases the activity of a GTPase.
	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: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:0016192	vesicle-mediated transport	A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0031410	cytoplasmic vesicle	A vesicle found in the cytoplasm of a cell.
	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: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: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:0055037	recycling endosome	An organelle consisting of a network of tubules that functions in targeting molecules, such as receptors transporters and lipids, to the plasma membrane.

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	Cis Peptide Bonds
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	1tu3
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	RAB5A_HUMAN \| P20339
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	RABE1_HUMAN \| Q15276
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	RABE1_HUMAN \| Q15276
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(no "Related Entries Specified in the PDB File" available for 1TU3)

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (2, 10)

Sites (10, 10)

SS Bonds (0, 0)

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Exons (5, 25)

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SCOP Domains (2, 10)

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