4FMD - JenaLib

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Biological Unit 1 (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   ESPG-RAB1 COMPLEX STRUCTURE AT 3.05 A

Authors :   F. Shao, Y. Zhu

Date :   16 Jun 12 (Deposition) - 05 Sep 12 (Release) - 03 Oct 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.05

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

Keywords :   Alpha-Beta Fold, Rab1-Gap, Rab1, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. Dong, Y. Zhu, Q. Lu, L. Hu, Y. Zheng, F. Shao
Structurally Distinct Bacterial Tbc-Like Gaps Link Arf Gtpase To Rab1 Inactivation To Counteract Host Defenses.
Cell(Cambridge, Mass. ) V. 150 1029 2012
PubMed-ID: 22939626 | Reference-DOI: 10.1016/J.CELL.2012.06.050

Molecule 1 - ESPG PROTEIN
	Chains	:	A, C, E
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-6P-2
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	ESPG
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Strain	:	O157

Molecule 2 - RAS-RELATED PROTEIN RAB-1A
	Chains	:	B, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	RAB1, RAB1A
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	YPT1-RELATED PROTEIN

Molecule 3 - RAS-RELATED PROTEIN RAB-1A
	Chains	:	F
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	RAB1, RAB1A
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	YPT1-RELATED PROTEIN

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	C	D	E	F
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D
Biological Unit 3 (1x)	:					E	F

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 11)

No.	Name	Count	Type	Full Name
1	AF3	3	Ligand/Ion	ALUMINUM FLUORIDE
2	GDP	3	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
3	MG	3	Ligand/Ion	MAGNESIUM ION
4	PEG	1	Ligand/Ion	DI(HYDROXYETHYL)ETHER
5	PGE	1	Ligand/Ion	TRIETHYLENE GLYCOL

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	AF3	1	Ligand/Ion	ALUMINUM FLUORIDE
2	GDP	1	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	PEG	-1	Ligand/Ion	DI(HYDROXYETHYL)ETHER
5	PGE	-1	Ligand/Ion	TRIETHYLENE GLYCOL

Biological Unit 2 (3, 3)

No.	Name	Count	Type	Full Name
1	AF3	1	Ligand/Ion	ALUMINUM FLUORIDE
2	GDP	1	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	PEG	-1	Ligand/Ion	DI(HYDROXYETHYL)ETHER
5	PGE	1	Ligand/Ion	TRIETHYLENE GLYCOL

Biological Unit 3 (3, 3)

No.	Name	Count	Type	Full Name
1	AF3	1	Ligand/Ion	ALUMINUM FLUORIDE
2	GDP	1	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	PEG	1	Ligand/Ion	DI(HYDROXYETHYL)ETHER
5	PGE	-1	Ligand/Ion	TRIETHYLENE GLYCOL

Asymmetric Unit (11, 11)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ARG A:208 , GLN A:293 , HOH A:401 , SER B:20 , LYS B:24 , THR B:43 , GLY B:69 , GDP B:202 , MG B:203 , HOH B:302	BINDING SITE FOR RESIDUE AF3 B 201
02	AC2	SOFTWARE	ARG A:208 , THR A:239 , GLY B:21 , GLY B:23 , LYS B:24 , SER B:25 , CYS B:26 , TYR B:36 , GLU B:38 , ASN B:124 , LYS B:125 , ASP B:127 , SER B:154 , ALA B:155 , LYS B:156 , AF3 B:201 , MG B:203 , HOH B:301	BINDING SITE FOR RESIDUE GDP B 202
03	AC3	SOFTWARE	SER B:25 , THR B:43 , AF3 B:201 , GDP B:202 , HOH B:301 , HOH B:302	BINDING SITE FOR RESIDUE MG B 203
04	AC4	SOFTWARE	THR A:301 , HIS A:304 , GLU A:305 , GLU C:305	BINDING SITE FOR RESIDUE PGE C 401
05	AC5	SOFTWARE	ARG C:208 , GLN C:293 , HOH C:501 , SER D:20 , GLY D:21 , LYS D:24 , THR D:43 , THR D:67 , GLY D:69 , GDP D:202 , MG D:203 , HOH D:302	BINDING SITE FOR RESIDUE AF3 D 201
06	AC6	SOFTWARE	ARG C:208 , THR C:239 , GLY D:21 , VAL D:22 , GLY D:23 , LYS D:24 , SER D:25 , CYS D:26 , TYR D:36 , GLU D:38 , ASN D:124 , LYS D:125 , ASP D:127 , LEU D:128 , SER D:154 , ALA D:155 , LYS D:156 , AF3 D:201 , MG D:203 , HOH D:301 , HOH D:302	BINDING SITE FOR RESIDUE GDP D 202
07	AC7	SOFTWARE	SER D:25 , THR D:43 , AF3 D:201 , GDP D:202 , HOH D:301 , HOH D:302	BINDING SITE FOR RESIDUE MG D 203
08	AC8	SOFTWARE	THR E:301 , HIS E:304 , GLU E:305	BINDING SITE FOR RESIDUE PEG E 401
09	AC9	SOFTWARE	ARG E:208 , GLN E:293 , HOH E:501 , ASP F:19 , SER F:20 , GLY F:21 , LYS F:24 , THR F:43 , GLY F:69 , GDP F:202 , MG F:203	BINDING SITE FOR RESIDUE AF3 F 201
10	BC1	SOFTWARE	ARG E:208 , THR E:239 , ASP F:19 , GLY F:21 , GLY F:23 , LYS F:24 , SER F:25 , CYS F:26 , TYR F:36 , ASN F:124 , LYS F:125 , ASP F:127 , SER F:154 , ALA F:155 , LYS F:156 , AF3 F:201 , MG F:203 , HOH F:301	BINDING SITE FOR RESIDUE GDP F 202
11	BC2	SOFTWARE	SER F:25 , THR F:43 , AF3 F:201 , GDP F:202 , HOH F:301	BINDING SITE FOR RESIDUE MG F 203

(no "SS Bond" information available for 4FMD)

(no "Cis Peptide Bond" information available for 4FMD)

(no "SAP(SNP)/Variant" information available for 4FMD)

(no "PROSITE Motif" information available for 4FMD)

(no "Exon" information available for 4FMD)

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:351
                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh......hhhhhhhhhhhhh..eee.....eeeeeeee.....eeeeeee....eeeeee.....eeeeee......hhhhhh..ee.....eeeee.......hhhhhhhhhhhhh...eee.................hhhhhhhhhh...eeee..eeehhhhhhhhhhhh.........hhhhhhhh.hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeeeeee.....eeeeeeeeeeee........eeeeeeeeeeee......hhhhhhhhh..eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fmd A  47 EMSCAEKLLKVLSFGLWNPTYSRSERQSFQELLTVLEPVYPLPNELGRVSARFSDGSSLRISVTNSESIEAEIRTPNNEKITVLLESNEQNRLLQSLPIDRHMPYIQVHRALSEMDLTDTTSMRNLLGFTSKLSTTLIPHNAQTDPLSGPTPFSSIFMDTCRGLGNAKLSLNGVDIPANAQMLLRDALGLKDTHSSPTRNVIDHGISRHDAEQIARESSGSDKQKAEVVEFLCHPEAATAICSAFYQSFNVPALTLTHERISKASEYNAERSLDTPNACINISISQSSDGNIYVTSHTGVLIMAPEDRPNEMGMLTNRTSYEVPQGVKCTIDEMVRALQPRYAASETYLQN 397
                                    56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396

Chain B from PDB  Type:PROTEIN  Length:171
                                                                                                                                                                                                           
               SCOP domains d4fmdb_ B: Rab1a                                                                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeee....hhhhhhhhhhhh...........eeeeeeeeee..eeeeeeeeee..hhhhhhhhhhhhhhh.eeeeeee..hhhhhhhhhhhhhhhhhhh....eeeeeee..........hhhhhhhhhhhh...eee.......hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fmd B   6 PEYDYLFKLLLIGDSGVGKSCLLLRFADDTYTESYISTIGVDFKIRTIELDGKTIKLQIWDTAGQERFRTITSSYYRGAHGIIVVYDVTDQESFNNVKQWLQEIDRYASENVNKLLVGNKCDLTTKKVVDYTTAKEFADSLGIPFLETSAKNATNVEQSFMTMAAEIKKRM 176
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175

Chain C from PDB  Type:PROTEIN  Length:351
                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh......hhhhhhhhhhhhh..eee.....eeeeeeee.....eeeeeee....eeeeee.....eeeeee......hhhhhh..ee.....eeee........hhhhhhhhhhhhh...eee.................hhhhhhhhhh....eee..eeehhhhhhhhhhhh.........hhhhhhhh.hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeeeeee.....eeeeeeeeeeee........eeeeeeeeeeee......hhhhhhhhh..eeeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fmd C  47 EMSCAEKLLKVLSFGLWNPTYSRSERQSFQELLTVLEPVYPLPNELGRVSARFSDGSSLRISVTNSESIEAEIRTPNNEKITVLLESNEQNRLLQSLPIDRHMPYIQVHRALSEMDLTDTTSMRNLLGFTSKLSTTLIPHNAQTDPLSGPTPFSSIFMDTCRGLGNAKLSLNGVDIPANAQMLLRDALGLKDTHSSPTRNVIDHGISRHDAEQIARESSGSDKQKAEVVEFLCHPEAATAICSAFYQSFNVPALTLTHERISKASEYNAERSLDTPNACINISISQSSDGNIYVTSHTGVLIMAPEDRPNEMGMLTNRTSYEVPQGVKCTIDEMVRALQPRYAASETYLQN 397
                                    56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396

Chain D from PDB  Type:PROTEIN  Length:171
                                                                                                                                                                                                           
               SCOP domains d4fmdd_ D: Rab1a                                                                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeee....hhhhhhhhhhhh...........eeeeeeeeee..eeeeeeeeee..hhhhhhhhhh......eeeeeee..hhhhhhhhhhhhhhhhhhh....eeeeeee..........hhhhhhhhhhhh...eee.......hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fmd D   6 PEYDYLFKLLLIGDSGVGKSCLLLRFADDTYTESYISTIGVDFKIRTIELDGKTIKLQIWDTAGQERFRTITSSYYRGAHGIIVVYDVTDQESFNNVKQWLQEIDRYASENVNKLLVGNKCDLTTKKVVDYTTAKEFADSLGIPFLETSAKNATNVEQSFMTMAAEIKKRM 176
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175

Chain E from PDB  Type:PROTEIN  Length:350
                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh......hhhhhhhhhhhhh..eee.....eeeeeeee.....eeeeeee....eeeeee.....eeeee........hhhhh..ee.....eeee........hhhhhhhhhhhhh...eee.................hhhhhhhhhh...eeee..eeehhhhhhhhhhh..........hhhhhhhh.hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeeeeee.....eeeeeeeeeeee........eeeeeeeeeeee......hhhhhhhhh..eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fmd E  47 EMSCAEKLLKVLSFGLWNPTYSRSERQSFQELLTVLEPVYPLPNELGRVSARFSDGSSLRISVTNSESIEAEIRTPNNEKITVLLESNEQNRLLQSLPIDRHMPYIQVHRALSEMDLTDTTSMRNLLGFTSKLSTTLIPHNAQTDPLSGPTPFSSIFMDTCRGLGNAKLSLNGVDIPANAQMLLRDALGLKDTHSSPTRNVIDHGISRHDAEQIARESSGSDKQKAEVVEFLCHPEAATAICSAFYQSFNVPALTLTHERISKASEYNAERSLDTPNACINISISQSSDGNIYVTSHTGVLIMAPEDRPNEMGMLTNRTSYEVPQGVKCTIDEMVRALQPRYAASETYLQ 396
                                    56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396

Chain F from PDB  Type:PROTEIN  Length:149
                                                                                                                                                                                     
               SCOP domains d4fmdf_ F: Rab1a                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee....hhhhhhhhhhhh........eee....eee..hhhhhhhhhhhhhhh.eeeeeee..hhhhhhhhhhhhhhhhhhh....eeeeeee..........hhhhhhhhhhhhh..eee.......hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fmd F  13 KLLLIGDSGVGKSCLLLRFADDTYTISTIGVDFKIRIWDTAGQERFRTITSSYYRGAHGIIVVYDVTDQESFNNVKQWLQEIDRYASENVNKLLVGNKCDLTTKKVVDYTTAKEFADSLGIPFLETSAKNATNVEQSFMTMAAEIKKRM 176
                                    22        32    ||  45     || 67        77        87        97       107       117       127       137       147       157       167         
                                                   37|        51|                                                                                                                
                                                    41         64

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	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: Rab1a (3)

Human (Homo sapiens) [TaxId: 9606] (3)

1a	d4fmdb_	B:
1b	d4fmdd_	D:
1c	d4fmdf_	F:

(no "CATH Domain" information available for 4FMD)

(no "Pfam Domain" information available for 4FMD)

Asymmetric Unit(hide GO term definitions)

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 11)

Sites (11, 11)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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Gene Ontology (45, 52)

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