5JCP - 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)

Title :   RHOGAP DOMAIN OF ARAP3 IN COMPLEX WITH RHOA IN THE TRANSITION STATE

Authors :   H. Bao, F. Li, C. Wang, N. Wang, Y. Jiang, Y. Tang, J. Wu, Y. Shi

Date :   15 Apr 16 (Deposition) - 22 Jun 16 (Release) - 17 Aug 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym. Unit : A,B
Biol. Unit 1: B  (1x)
Biol. Unit 2: A  (1x)

Keywords :   Rhoa, Rhogap, Arap3, Signaling Protein, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Bao, F. Li, C. Wang, N. Wang, Y. Jiang, Y. Tang, J. Wu, Y. Shi
Structural Basis For The Specific Recognition Of Rhoa By Th Dual Gtpase-Activating Protein Arap3
J. Biol. Chem. V. 291 16709 2016
PubMed-ID: 27311713 | Reference-DOI: 10.1074/JBC.M116.736140

Molecule 1 - ARF-GAP WITH RHO-GAP DOMAIN, ANK REPEAT AND PH DOMAIN- CONTAINING PROTEIN 3,LINKER,TRANSFORMING PROTEIN RHOA
	Chains	:	B, A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'
	Expression System Strain	:	BL21-GOLD(DE3)PLYSS AG
	Expression System Taxid	:	866768
	Fragment	:	UNP RESIDUES 906-1107,UNP RESIDUES 2-181
	Gene	:	ARAP3, RHOA
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS, SYNTHETIC CONSTRUCT
	Organism Taxid	:	9606, 32630

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:		B
Biological Unit 2 (1x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 6)

No.	Name	Count	Type	Full Name
1	ALF	2	Ligand/Ion	TETRAFLUOROALUMINATE ION
2	GDP	2	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
3	MG	2	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	ALF	1	Ligand/Ion	TETRAFLUOROALUMINATE ION
2	GDP	1	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	ALF	1	Ligand/Ion	TETRAFLUOROALUMINATE ION
2	GDP	1	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA B:15 , CYS B:16 , GLY B:17 , LYS B:18 , THR B:19 , CYS B:20 , LYS B:118 , ASP B:120 , LEU B:121 , SER B:160 , ALA B:161 , LYS B:162 , ARG B:942 , MG B:1202 , ALF B:1203 , HOH B:1312 , HOH B:1320 , HOH B:1388	binding site for residue GDP B 1201
2	AC2	SOFTWARE	THR B:19 , GDP B:1201 , ALF B:1203 , HOH B:1312 , HOH B:1320	binding site for residue MG B 1202
3	AC3	SOFTWARE	GLY B:14 , ALA B:15 , LYS B:18 , GLY B:62 , GLN B:63 , ARG B:942 , GDP B:1201 , MG B:1202 , HOH B:1304 , HOH B:1312 , HOH B:1320	binding site for residue ALF B 1203
4	AC4	SOFTWARE	ALA A:15 , CYS A:16 , GLY A:17 , LYS A:18 , THR A:19 , CYS A:20 , LYS A:118 , ASP A:120 , LEU A:121 , SER A:160 , ALA A:161 , LYS A:162 , ARG A:942 , MG A:1202 , ALF A:1203 , HOH A:1307 , HOH A:1323 , HOH A:1353 , HOH A:1365	binding site for residue GDP A 1201
5	AC5	SOFTWARE	THR A:19 , GDP A:1201 , ALF A:1203 , HOH A:1307 , HOH A:1323	binding site for residue MG A 1202
6	AC6	SOFTWARE	GLY A:14 , ALA A:15 , LYS A:18 , GLY A:62 , GLN A:63 , ARG A:942 , GDP A:1201 , MG A:1202 , HOH A:1305 , HOH A:1307 , HOH A:1323	binding site for residue ALF A 1203

(no "SS Bond" information available for 5JCP)

(no "Cis Peptide Bond" information available for 5JCP)

(no "SAP(SNP)/Variant" information available for 5JCP)

(no "PROSITE Motif" information available for 5JCP)

(no "Exon" information available for 5JCP)

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:361
                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh.......hhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh..eeeeeeeee....hhhhhhhhhh.eeeeeee..eeeeeeee....hhhhh.hhhhhh....eeeeeee..hhhhhhhhhhhhhhhhhhhh....eeeeeehhhhh.hhhhhhhhhhh.....hhhhhhhhhhhhh..eeee.......hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5jcp A  906 GTGLQEQQMSRGDIPIIVDACISFVTQHGLRLEGVYRKGGARARSLRLLAEFRRDARSVKLRPGEHFVEDVTDTLKRFFRELDDPVTSARLLPRWREAAELPQKNQRLEKYKDVIGCLPRVNRRTLATLIGHLYRVQKCAALNQMCTRNLALLFAPSVFQTDGRGEHEVRVLQELIDGYISVFDIDSDQVAQIDLEVAIRKKLVIVGDGACGKTCLLIVNSNYVADIEVDGKQVELALWDTAGQEDYDRLRPLSYPDTDVILMCFSIDSPDSLENIPEKWTPEVKHFCPNVPIILVGNKKDLRNDEHTRRELAKMKQEPVKPEEGRDMANRIGAFGYMECSAKTKDGVREVFEMATRAALQ  180
                                   915       925       935       945       955       965       975       985       995      1005      1015      1025      1035      1045      1055      1065      1075      1085      1095      || 5        15        25||      49        59        69        79        89        99       109       119       129       139       149       159       169       179 
                                                                                                                                                                                                                             1102|                     26|                                                                                                                                           
                                                                                                                                                                                                                                 3                      41

Chain B from PDB  Type:PROTEIN  Length:359
                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh.......hhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.eeeeeeeee....hhhhhhhhhh.eeeeeee..eeeeeeee....hhhhh.hhhhhh....eeeeeee..hhhhhhhhhhhhhhhhhhhh....eeeeeehhhhh.hhhhhhhhhhh.....hhhhhhhhhhhhh..eeee.......hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5jcp B  906 GTGLQEQQMSRGDIPIIVDACISFVTQHGLRLEGVYRKGGARARSLRLLAEFRRDARSVKLRPGEHFVEDVTDTLKRFFRELDDPVTSARLLPRWREAAELPQKNQRLEKYKDVIGCLPRVNRRTLATLIGHLYRVQKCAALNQMCTRNLALLFAPSVFQTDGRGEHEVRVLQELIDGYISVFDIDSDQVAQIDLAIRKKLVIVGDGACGKTCLLIVNSNYVADIEVDGKQVELALWDTAGQEDYDRLRPLSYPDTDVILMCFSIDSPDSLENIPEKWTPEVKHFCPNVPIILVGNKKDLRNDEHTRRELAKMKQEPVKPEEGRDMANRIGAFGYMECSAKTKDGVREVFEMATRAALQ  180
                                   915       925       935       945       955       965       975       985       995      1005      1015      1025      1035      1045      1055      1065      1075      1085      1095    ||   7        17        41        51        61        71        81        91       101       111       121       131       141       151       161       171         
                                                                                                                                                                                                                           1100|                     26|                                                                                                                                           
                                                                                                                                                                                                                               3                      41

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 '\|'

(no "SCOP Domain" information available for 5JCP)

(no "CATH Domain" information available for 5JCP)

(no "Pfam Domain" information available for 5JCP)

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		ALF	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		GDP	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5jcp)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	5jcp
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	ARAP3_HUMAN \| Q8WWN8
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	RHOA_HUMAN \| P61586
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	ARAP3_HUMAN \| Q8WWN8
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	RHOA_HUMAN \| P61586
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

(no "Related Entries Specified in the PDB File" available for 5JCP)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (81, 90)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File