3LAW - JenaLib

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)

Biological Unit 4 (Jmol Viewer)

Biological Unit 5 (Jmol Viewer)

Title :   STRUCTURE OF GTP-BOUND L129F MUTANT RAB7

Authors :   B. A. Mccray, E. Skordalakes, J. P. Taylor

Date :   07 Jan 10 (Deposition) - 26 Jan 10 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

Chains :   Asym. Unit : A,B,C,D,E
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)
Biol. Unit 5: E  (1x)

Keywords :   Protein - Nucleotide Complex, Protein Mutant, Charcot-Marie-Tooth Disease, Cytoplasmic Vesicle, Disease Mutation, Endosome, Gtp- Binding, Lipoprotein, Lysosome, Methylation, Neuropathy, Nucleotide- Binding, Phosphoprotein, Prenylation, Protein Transport, Proton Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. A. Mccray, E. Skordalakes, J. P. Taylor
Disease Mutations In Rab7 Result In Unregulated Nucleotide Exchange And Inappropriate Activation.
Hum. Mol. Genet. V. 19 1033 2010
PubMed-ID: 20028791 | Reference-DOI: 10.1093/HMG/DDP567

Molecule 1 - RAS-RELATED PROTEIN RAB-7A
	Chains	:	A, B, C, D, E
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	RAB7A, RAB7
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1	2	3	4	5
Asymmetric Unit	:	A	B	C	D	E
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C
Biological Unit 4 (1x)	:				D
Biological Unit 5 (1x)	:					E

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, 1)

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

Biological Unit 2 (1, 1)

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

Biological Unit 3 (1, 1)

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

Biological Unit 4 (1, 1)

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

Biological Unit 5 (1, 1)

No.	Name	Count	Type	Full Name
1	GNP	1	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	THR A:22 , THR A:40 , ASP A:63 , THR A:64 , GNP A:1400	BINDING SITE FOR RESIDUE MG A 1401
02	AC2	SOFTWARE	ASP A:16 , SER A:17 , GLY A:18 , VAL A:19 , GLY A:20 , LYS A:21 , THR A:22 , SER A:23 , PHE A:33 , SER A:34 , ASN A:35 , TYR A:37 , THR A:40 , GLY A:66 , ASN A:125 , LYS A:126 , ASP A:128 , PHE A:129 , SER A:155 , ALA A:156 , LYS A:157 , HOH A:216 , MG A:1401 , PHE B:45	BINDING SITE FOR RESIDUE GNP A 1400
03	AC3	SOFTWARE	THR B:22 , THR B:40 , ASP B:63 , THR B:64 , GNP B:1400	BINDING SITE FOR RESIDUE MG B 1401
04	AC4	SOFTWARE	SER B:17 , GLY B:18 , VAL B:19 , GLY B:20 , LYS B:21 , THR B:22 , SER B:23 , PHE B:33 , SER B:34 , ASN B:35 , TYR B:37 , THR B:40 , GLY B:66 , ASN B:125 , LYS B:126 , ASP B:128 , PHE B:129 , SER B:155 , ALA B:156 , LYS B:157 , MG B:1401 , THR D:47	BINDING SITE FOR RESIDUE GNP B 1400
05	AC5	SOFTWARE	THR C:22 , THR C:40 , ASP C:63 , GNP C:1400	BINDING SITE FOR RESIDUE MG C 1401
06	AC6	SOFTWARE	THR A:47 , SER C:17 , GLY C:18 , VAL C:19 , GLY C:20 , LYS C:21 , THR C:22 , SER C:23 , PHE C:33 , SER C:34 , ASN C:35 , TYR C:37 , THR C:40 , GLY C:66 , ASN C:125 , LYS C:126 , ASP C:128 , PHE C:129 , SER C:155 , ALA C:156 , LYS C:157 , MG C:1401	BINDING SITE FOR RESIDUE GNP C 1400
07	AC7	SOFTWARE	THR D:22 , THR D:40 , ASP D:63 , THR D:64 , GNP D:1400	BINDING SITE FOR RESIDUE MG D 1401
08	AC8	SOFTWARE	SER D:17 , GLY D:18 , VAL D:19 , GLY D:20 , LYS D:21 , THR D:22 , SER D:23 , SER D:34 , ASN D:35 , TYR D:37 , ALA D:39 , THR D:40 , GLY D:66 , ASN D:125 , LYS D:126 , ASP D:128 , PHE D:129 , ALA D:156 , LYS D:157 , MG D:1401 , PHE E:45 , THR E:47	BINDING SITE FOR RESIDUE GNP D 1400
09	AC9	SOFTWARE	THR E:22 , THR E:40 , ASP E:63 , THR E:64 , GNP E:1400	BINDING SITE FOR RESIDUE MG E 1401
10	BC1	SOFTWARE	PHE C:45 , ASP E:16 , SER E:17 , GLY E:18 , VAL E:19 , GLY E:20 , LYS E:21 , THR E:22 , SER E:23 , PHE E:33 , SER E:34 , ASN E:35 , TYR E:37 , THR E:40 , ALA E:65 , GLY E:66 , ASN E:125 , LYS E:126 , ASP E:128 , PHE E:129 , SER E:155 , ALA E:156 , LYS E:157 , MG E:1401	BINDING SITE FOR RESIDUE GNP E 1400

(no "SS Bond" information available for 3LAW)

Asymmetric Unit

No.	Residues
1	Ser A:72	-	Leu A:73
2	Gly D:74	-	Val D:75
3	Ser E:72	-	Leu E:73

Asymmetric Unit (5, 25)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_037886	K	32	E	RAB7A_HUMAN	Polymorphism	11549759	A/B/C/D/E	K	32	E
2	UniProt	VAR_018722	L	129	F	RAB7A_HUMAN	Disease (CMT2B)	121909078	A/B/C/D/E	F	129	F
3	UniProt	VAR_037887	K	157	N	RAB7A_HUMAN	Disease (CMT2B)	121909081	A/B/C/D/E	K	157	N
4	UniProt	VAR_037888	N	161	T	RAB7A_HUMAN	Disease (CMT2B)	121909080	A/B/C/D/E	N	161	T
5	UniProt	VAR_018723	V	162	M	RAB7A_HUMAN	Disease (CMT2B)	121909079	A/B/C/D/E	V	162	M

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (5, 5)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_037886	K	32	E	RAB7A_HUMAN	Polymorphism	11549759	A	K	32	E
2	UniProt	VAR_018722	L	129	F	RAB7A_HUMAN	Disease (CMT2B)	121909078	A	F	129	F
3	UniProt	VAR_037887	K	157	N	RAB7A_HUMAN	Disease (CMT2B)	121909081	A	K	157	N
4	UniProt	VAR_037888	N	161	T	RAB7A_HUMAN	Disease (CMT2B)	121909080	A	N	161	T
5	UniProt	VAR_018723	V	162	M	RAB7A_HUMAN	Disease (CMT2B)	121909079	A	V	162	M

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (5, 5)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_037886	K	32	E	RAB7A_HUMAN	Polymorphism	11549759	B	K	32	E
2	UniProt	VAR_018722	L	129	F	RAB7A_HUMAN	Disease (CMT2B)	121909078	B	F	129	F
3	UniProt	VAR_037887	K	157	N	RAB7A_HUMAN	Disease (CMT2B)	121909081	B	K	157	N
4	UniProt	VAR_037888	N	161	T	RAB7A_HUMAN	Disease (CMT2B)	121909080	B	N	161	T
5	UniProt	VAR_018723	V	162	M	RAB7A_HUMAN	Disease (CMT2B)	121909079	B	V	162	M

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 3 (5, 5)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_037886	K	32	E	RAB7A_HUMAN	Polymorphism	11549759	C	K	32	E
2	UniProt	VAR_018722	L	129	F	RAB7A_HUMAN	Disease (CMT2B)	121909078	C	F	129	F
3	UniProt	VAR_037887	K	157	N	RAB7A_HUMAN	Disease (CMT2B)	121909081	C	K	157	N
4	UniProt	VAR_037888	N	161	T	RAB7A_HUMAN	Disease (CMT2B)	121909080	C	N	161	T
5	UniProt	VAR_018723	V	162	M	RAB7A_HUMAN	Disease (CMT2B)	121909079	C	V	162	M

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 4 (5, 5)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_037886	K	32	E	RAB7A_HUMAN	Polymorphism	11549759	D	K	32	E
2	UniProt	VAR_018722	L	129	F	RAB7A_HUMAN	Disease (CMT2B)	121909078	D	F	129	F
3	UniProt	VAR_037887	K	157	N	RAB7A_HUMAN	Disease (CMT2B)	121909081	D	K	157	N
4	UniProt	VAR_037888	N	161	T	RAB7A_HUMAN	Disease (CMT2B)	121909080	D	N	161	T
5	UniProt	VAR_018723	V	162	M	RAB7A_HUMAN	Disease (CMT2B)	121909079	D	V	162	M

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 5 (5, 5)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_037886	K	32	E	RAB7A_HUMAN	Polymorphism	11549759	E	K	32	E
2	UniProt	VAR_018722	L	129	F	RAB7A_HUMAN	Disease (CMT2B)	121909078	E	F	129	F
3	UniProt	VAR_037887	K	157	N	RAB7A_HUMAN	Disease (CMT2B)	121909081	E	K	157	N
4	UniProt	VAR_037888	N	161	T	RAB7A_HUMAN	Disease (CMT2B)	121909080	E	N	161	T
5	UniProt	VAR_018723	V	162	M	RAB7A_HUMAN	Disease (CMT2B)	121909079	E	V	162	M

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(no "PROSITE Motif" information available for 3LAW)

Asymmetric Unit (5, 25)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000265062	1a	ENSE00001236693	chr3:128444965-128445202	238	RAB7A_HUMAN	-	0	0	-	-
1.2c	ENST00000265062	2c	ENSE00002193380	chr3:128514203-128514263	61	RAB7A_HUMAN	1-18	18	5	A:6-18 B:6-18 C:5-18 D:5-18 E:6-18	13 13 14 14 13
1.3b	ENST00000265062	3b	ENSE00000903897	chr3:128516786-128516912	127	RAB7A_HUMAN	18-60	43	5	A:18-60 B:18-60 C:18-60 D:18-60 E:18-60	43 43 43 43 43
1.4c	ENST00000265062	4c	ENSE00000778026	chr3:128525215-128525433	219	RAB7A_HUMAN	61-133	73	5	A:61-133 B:61-133 C:61-133 D:61-133 E:61-133	73 73 73 73 73
1.5b	ENST00000265062	5b	ENSE00001047626	chr3:128526386-128526514	129	RAB7A_HUMAN	134-176	43	5	A:134-176 B:134-176 C:134-176 D:134-176 E:134-176	43 43 43 43 43
1.6f	ENST00000265062	6f	ENSE00001314364	chr3:128532170-128533639	1470	RAB7A_HUMAN	177-207	31	5	A:177-182 B:177-180 C:177-181 D:177-180 E:177-180	6 4 5 4 4

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:177
 aligned with RAB7A_HUMAN | P51149 from UniProtKB/Swiss-Prot  Length:207

    Alignment length:177
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       
          RAB7A_HUMAN     6 KVLLKVIILGDSGVGKTSLMNQYVNKKFSNQYKATIGADFLTKEVMVDDRLVTMQIWDTAGQERFQSLGVAFYRGADCCVLVFDVTAPNTFKTLDSWRDEFLIQASPRDPENFPFVVLGNKIDLENRQVATKRAQAWCYSKNNIPYFETSAKEAINVEQAFQTIARNALKQETEVEL 182
               SCOP domains d3lawa_ A: automated matches                                                                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.....hhhhhhhhhhhh............eeeeeeeee..eeeeeeeee...................eeeeeee..hhhhhhhhhhhhhhhhhhhh..hhhhh.eeeeee.........hhhhhhhhhhhh....eeee......hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------E------------------------------------------------------------------------------------------------F---------------------------N---TM-------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2c    ------------------------------------------Exon 1.4c  PDB: A:61-133 UniProt: 61-133                                 Exon 1.5b  PDB: A:134-176 UniProt: 134-176 1.6f   Transcript 1 (1)
           Transcript 1 (2) ------------Exon 1.3b  PDB: A:18-60 UniProt: 18-60     -------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 3law A   6 KVLLKVIILGDSGVGKTSLMNQYVNKKFSNQYKATIGADFLTKEVMVDDRLVTMQIWDTAGQERFQSLGVAFYRGADCCVLVFDVTAPNTFKTLDSWRDEFLIQASPRDPENFPFVVLGNKIDFENRQVATKRAQAWCYSKNNIPYFETSAKEAINVEQAFQTIARNALKQETEVEL 182
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175

Chain B from PDB  Type:PROTEIN  Length:175
 aligned with RAB7A_HUMAN | P51149 from UniProtKB/Swiss-Prot  Length:207

    Alignment length:175
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175     
          RAB7A_HUMAN     6 KVLLKVIILGDSGVGKTSLMNQYVNKKFSNQYKATIGADFLTKEVMVDDRLVTMQIWDTAGQERFQSLGVAFYRGADCCVLVFDVTAPNTFKTLDSWRDEFLIQASPRDPENFPFVVLGNKIDLENRQVATKRAQAWCYSKNNIPYFETSAKEAINVEQAFQTIARNALKQETEV 180
               SCOP domains d3lawb_ B: automated matches                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.....hhhhhhhhhh..............eeeeeeeee..eeeeeeeee...................eeeeeee...hhhhhhhhhhhhhhhhhh.........eeeeee.........hhhhhhhhhhh.....eeee......hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------E------------------------------------------------------------------------------------------------F---------------------------N---TM------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2c    ------------------------------------------Exon 1.4c  PDB: B:61-133 UniProt: 61-133                                 Exon 1.5b  PDB: B:134-176 UniProt: 134-176 1.6f Transcript 1 (1)
           Transcript 1 (2) ------------Exon 1.3b  PDB: B:18-60 UniProt: 18-60     ------------------------------------------------------------------------------------------------------------------------ Transcript 1 (2)
                 3law B   6 KVLLKVIILGDSGVGKTSLMNQYVNKKFSNQYKATIGADFLTKEVMVDDRLVTMQIWDTAGQERFQSLGVAFYRGADCCVLVFDVTAPNTFKTLDSWRDEFLIQASPRDPENFPFVVLGNKIDFENRQVATKRAQAWCYSKNNIPYFETSAKEAINVEQAFQTIARNALKQETEV 180
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175

Chain C from PDB  Type:PROTEIN  Length:177
 aligned with RAB7A_HUMAN | P51149 from UniProtKB/Swiss-Prot  Length:207

    Alignment length:177
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       
          RAB7A_HUMAN     5 KKVLLKVIILGDSGVGKTSLMNQYVNKKFSNQYKATIGADFLTKEVMVDDRLVTMQIWDTAGQERFQSLGVAFYRGADCCVLVFDVTAPNTFKTLDSWRDEFLIQASPRDPENFPFVVLGNKIDLENRQVATKRAQAWCYSKNNIPYFETSAKEAINVEQAFQTIARNALKQETEVE 181
               SCOP domains d3lawc_ C: automated matches                                                                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee....hhhhhhhhhhhh............eeeeeeeee..eeeeeeeee...hhhhh...hhhhh.eeeeeeeee..hhhhhhhhhhhhhhhhhhhh........eeeeee.........hhhhhhhhhhhh....eeee......hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------E------------------------------------------------------------------------------------------------F---------------------------N---TM------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2c     ------------------------------------------Exon 1.4c  PDB: C:61-133 UniProt: 61-133                                 Exon 1.5b  PDB: C:134-176 UniProt: 134-176 1.6f  Transcript 1 (1)
           Transcript 1 (2) -------------Exon 1.3b  PDB: C:18-60 UniProt: 18-60     ------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 3law C   5 KKVLLKVIILGDSGVGKTSLMNQYVNKKFSNQYKATIGADFLTKEVMVDDRLVTMQIWDTAGQERFQSLGVAFYRGADCCVLVFDVTAPNTFKTLDSWRDEFLIQASPRDPENFPFVVLGNKIDFENRQVATKRAQAWCYSKNNIPYFETSAKEAINVEQAFQTIARNALKQETEVE 181
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174

Chain D from PDB  Type:PROTEIN  Length:176
 aligned with RAB7A_HUMAN | P51149 from UniProtKB/Swiss-Prot  Length:207

    Alignment length:176
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174      
          RAB7A_HUMAN     5 KKVLLKVIILGDSGVGKTSLMNQYVNKKFSNQYKATIGADFLTKEVMVDDRLVTMQIWDTAGQERFQSLGVAFYRGADCCVLVFDVTAPNTFKTLDSWRDEFLIQASPRDPENFPFVVLGNKIDLENRQVATKRAQAWCYSKNNIPYFETSAKEAINVEQAFQTIARNALKQETEV 180
               SCOP domains d3lawd_ D: automated matches                                                                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee.....hhhhhhhhhhhh...........eeeeeeeee....eeeeeeeee..................eeeeeee..hhhhhhhhhhhhhhhhhhhh..hhhhh.eeeeee.........hhhhhhhhhhh.....eeee......hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------E------------------------------------------------------------------------------------------------F---------------------------N---TM------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2c     ------------------------------------------Exon 1.4c  PDB: D:61-133 UniProt: 61-133                                 Exon 1.5b  PDB: D:134-176 UniProt: 134-176 1.6f Transcript 1 (1)
           Transcript 1 (2) -------------Exon 1.3b  PDB: D:18-60 UniProt: 18-60     ------------------------------------------------------------------------------------------------------------------------ Transcript 1 (2)
                 3law D   5 KKVLLKVIILGDSGVGKTSLMNQYVNKKFSNQYKATIGADFLTKEVMVDDRLVTMQIWDTAGQERFQSLGVAFYRGADCCVLVFDVTAPNTFKTLDSWRDEFLIQASPRDPENFPFVVLGNKIDFENRQVATKRAQAWCYSKNNIPYFETSAKEAINVEQAFQTIARNALKQETEV 180
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174

Chain E from PDB  Type:PROTEIN  Length:175
 aligned with RAB7A_HUMAN | P51149 from UniProtKB/Swiss-Prot  Length:207

    Alignment length:175
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175     
          RAB7A_HUMAN     6 KVLLKVIILGDSGVGKTSLMNQYVNKKFSNQYKATIGADFLTKEVMVDDRLVTMQIWDTAGQERFQSLGVAFYRGADCCVLVFDVTAPNTFKTLDSWRDEFLIQASPRDPENFPFVVLGNKIDLENRQVATKRAQAWCYSKNNIPYFETSAKEAINVEQAFQTIARNALKQETEV 180
               SCOP domains d3lawe_ E: automated matches                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----Ras-3lawE01 E:10-175                                                                                                                                                  ----- Pfam domains (1)
           Pfam domains (2) ----Ras-3lawE02 E:10-175                                                                                                                                                  ----- Pfam domains (2)
           Pfam domains (3) ----Ras-3lawE03 E:10-175                                                                                                                                                  ----- Pfam domains (3)
           Pfam domains (4) ----Ras-3lawE04 E:10-175                                                                                                                                                  ----- Pfam domains (4)
           Pfam domains (5) ----Ras-3lawE05 E:10-175                                                                                                                                                  ----- Pfam domains (5)
         Sec.struct. author .eeeeeeee.....hhhhhhhhhhhh............eeeeeeeee..eeeeeeeee...................eeeeeee..hhhhhhhhhhhhhhhhhhhh..hhhhh.eeeeee.........hhhhhhhhhhh.....eeee......hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------E------------------------------------------------------------------------------------------------F---------------------------N---TM------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2c    ------------------------------------------Exon 1.4c  PDB: E:61-133 UniProt: 61-133                                 Exon 1.5b  PDB: E:134-176 UniProt: 134-176 1.6f Transcript 1 (1)
           Transcript 1 (2) ------------Exon 1.3b  PDB: E:18-60 UniProt: 18-60     ------------------------------------------------------------------------------------------------------------------------ Transcript 1 (2)
                 3law E   6 KVLLKVIILGDSGVGKTSLMNQYVNKKFSNQYKATIGADFLTKEVMVDDRLVTMQIWDTAGQERFQSLGVAFYRGADCCVLVFDVTAPNTFKTLDSWRDEFLIQASPRDPENFPFVVLGNKIDFENRQVATKRAQAWCYSKNNIPYFETSAKEAINVEQAFQTIARNALKQETEV 180
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175

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: automated matches (173)

Human (Homo sapiens) [TaxId: 9606] (112)

1a	d3lawa_	A:
1b	d3lawb_	B:
1c	d3lawc_	C:
1d	d3lawd_	D:
1e	d3lawe_	E:

(no "CATH Domain" information available for 3LAW)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: Ras (176)

Homo sapiens (Human) (141)

1a	Ras-3lawE01	E:10-175
1b	Ras-3lawE02	E:10-175
1c	Ras-3lawE03	E:10-175
1d	Ras-3lawE04	E:10-175
1e	Ras-3lawE05	E:10-175

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E (RAB7A_HUMAN | P51149)

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:0048365	Rac GTPase binding	Interacting selectively and non-covalently with Rac protein, any member of the Rac subfamily of the Ras superfamily of monomeric GTPases.
	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:0019886	antigen processing and presentation of exogenous peptide antigen via MHC class II	The process in which an antigen-presenting cell expresses a peptide antigen of exogenous origin on its cell surface in association with an MHC class II protein complex. The peptide antigen is typically, but not always, processed from a whole protein.
	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:0045453	bone resorption	The process in which specialized cells known as osteoclasts degrade the organic and inorganic portions of bone, and endocytose and transport the degradation products.
	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:0008333	endosome to lysosome transport	The directed movement of substances from endosomes to lysosomes.
	GO:0007174	epidermal growth factor catabolic process	The chemical reactions and pathways resulting in the breakdown of epidermal growth factor (EGF), following internalization of the receptor-bound ligand into the signal-receiving cell. Full breakdown of epidermal growth factor results in a ligand that is unable to bind and activate its receptor.
	GO:0016042	lipid catabolic process	The chemical reactions and pathways resulting in the breakdown of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
	GO:0006629	lipid metabolic process	The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
	GO:0061724	lipophagy	The autophagic process in which lipid droplets are delivered to the vacuole and degraded in response to changing cellular conditions.
	GO:0090383	phagosome acidification	Any process that reduces the pH of the phagosome, measured by the concentration of the hydrogen ion.
	GO:0090382	phagosome maturation	A process that is carried out at the cellular level which results in the arrangement of constituent parts of a phagosome within a cell. Phagosome maturation begins with endocytosis and formation of the early phagosome and ends with the formation of the hybrid organelle, the phagolysosome.
	GO:0090385	phagosome-lysosome fusion	The creation of a phagolysosome from a phagosome and a lysosome.
	GO:1903543	positive regulation of exosomal secretion	Any process that activates or increases the frequency, rate or extent of exosomal secretion.
	GO:0045732	positive regulation of protein catabolic process	Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds.
	GO:0048524	positive regulation of viral process	Any process that activates or increases the frequency, rate or extent of a multi-organism process in which a virus is a participant.
	GO:0006622	protein targeting to lysosome	The process of directing proteins towards the lysosome using signals contained within the protein.
	GO:0022615	protein to membrane docking	The initial attachment of a protein to a target membrane, mediated by a proteins protruding from the target membrane. Docking requires only that the proteins come close enough to interact and adhere.
	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: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.
	GO:0019076	viral release from host cell	The dissemination of mature viral particles from the host cell, e.g. by cell lysis or the budding of virus particles from the cell membrane.
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:0097208	alveolar lamellar body	A specialized secretory organelle found in type II pneumocytes and involved in the synthesis, secretion, and reutilization of pulmonary surfactant.
	GO:0000421	autophagosome membrane	The lipid bilayer surrounding an autophagosome, a double-membrane-bounded vesicle in which endogenous cellular material is sequestered.
	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:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	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:0032419	extrinsic component of lysosome membrane	The component of an lysosome membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region.
	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: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:0031902	late endosome membrane	The lipid bilayer surrounding a late endosome.
	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: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:0033162	melanosome membrane	The lipid bilayer surrounding a melanosome.
	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:0034045	pre-autophagosomal structure membrane	A cellular membrane associated with the pre-autophagosomal structure.
	GO:0030904	retromer complex	A conserved hetero-pentameric membrane-associated complex involved in retrograde transport from endosomes to the Golgi apparatus. The budding yeast retromer comprises Vps35p, Vps29p, Vps26p, Vps5p, and Vps17p. The mammalian complex shows slight variation in composition compared to yeast, and comprises SNX1 or SNX2, SNX5 or SNX6, VPS26A or VPS26B, VPS29, and VPS35.
	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.
	GO:0005774	vacuolar membrane	The lipid bilayer surrounding the vacuole and separating its contents from the cytoplasm of the cell.

Asymmetric Unit
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	3law
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	RAB7A_HUMAN \| P51149
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	RAB7A_HUMAN \| P51149	:	1t91 1yhn

(no "Related Entries Specified in the PDB File" available for 3LAW)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 10)

Sites (10, 10)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

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Exons (5, 25)

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