4B3D - JenaLib

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Title :   HUMANISED MONOMERIC RADA IN COMPLEX WITH 5-METHYL INDOLE

Authors :   D. E. Scott, M. T. Ehebauer, T. Pukala, M. Marsh, T. L. Blundell, A. R. Venkitaraman, C. Abell, M. Hyvonen

Date :   23 Jul 12 (Deposition) - 06 Feb 13 (Release) - 27 Feb 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.59

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

Keywords :   Hydrolase, Recombinase, Thermostable, Peptide-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. E. Scott, M. T. Ehebauer, T. Pukala, M. Marsh, T. L. Blundell, A. R. Venkitaraman, C. Abell, M. Hyvonen
Using A Fragment-Based Approach To Target Protein-Protein Interactions.
Chembiochem V. 14 332 2013
PubMed-ID: 23344974 | Reference-DOI: 10.1002/CBIC.201200521

Molecule 1 - DNA REPAIR AND RECOMBINATION PROTEIN RADA
	Chains	:	A, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	CONTAINING PUBS520 PLASMID
	Expression System Vector	:	PBAT4
	Expression System Vector Type	:	PLASMID
	Fragment	:	ATPASE
	Mutation	:	YES
	Organism Scientific	:	PYROCOCCUS FURIOSUS
	Organism Taxid	:	2261
	Synonym	:	RADA

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 6)

No.	Name	Count	Type	Full Name
1	5MI	4	Ligand/Ion	5-METHYL INDOLE
2	PO4	2	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	5MI	2	Ligand/Ion	5-METHYL INDOLE
2	PO4	1	Ligand/Ion	PHOSPHATE ION

Biological Unit 2 (2, 3)

No.	Name	Count	Type	Full Name
1	5MI	2	Ligand/Ion	5-METHYL INDOLE
2	PO4	1	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:139 , PHE A:140 , GLY A:141 , SER A:142 , GLY A:143 , LYS A:144 , THR A:145 , HOH A:2049 , HOH A:2051 , HOH A:2054 , HOH A:2056 , HOH A:2347 , HOH A:2348	BINDING SITE FOR RESIDUE PO4 A1350
2	AC2	SOFTWARE	GLU C:139 , PHE C:140 , GLY C:141 , SER C:142 , GLY C:143 , LYS C:144 , THR C:145 , HOH C:2044 , HOH C:2048 , HOH C:2049 , HOH C:2050 , HOH C:2051 , HOH C:2318	BINDING SITE FOR RESIDUE PO4 C1350
3	AC3	SOFTWARE	MET C:169 , ILE C:171 , ALA C:203 , LEU C:214	BINDING SITE FOR RESIDUE 5MI C1351
4	AC4	SOFTWARE	MET A:169 , ILE A:171 , LEU A:214 , ALA A:218	BINDING SITE FOR RESIDUE 5MI A1351
5	AC5	SOFTWARE	ARG C:204 , LYS C:322 , HOH C:2292	BINDING SITE FOR RESIDUE 5MI C1352
6	AC6	SOFTWARE	ARG A:204 , PHE A:206 , LYS A:322	BINDING SITE FOR RESIDUE 5MI A1352

(no "SS Bond" information available for 4B3D)

Asymmetric Unit

No.	Residues
1	Asp A:238	-	Ser A:239
2	Asp C:238	-	Ser C:239

(no "SAP(SNP)/Variant" information available for 4B3D)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RECA_2	PS50162	RecA family profile 1.	RADA_PYRFU	109-285	2	A:109-285 C:109-285
2	RECA_3	PS50163	RecA family profile 2.	RADA_PYRFU	290-349	2	A:309-349 C:308-349

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RECA_2	PS50162	RecA family profile 1.	RADA_PYRFU	109-285	1	A:109-285 -
2	RECA_3	PS50163	RecA family profile 2.	RADA_PYRFU	290-349	1	A:309-349 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RECA_2	PS50162	RecA family profile 1.	RADA_PYRFU	109-285	1	- C:109-285
2	RECA_3	PS50163	RecA family profile 2.	RADA_PYRFU	290-349	1	- C:308-349

(no "Exon" information available for 4B3D)

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:213
 aligned with RADA_PYRFU | O74036 from UniProtKB/Swiss-Prot  Length:349

    Alignment length:242
                                   117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347  
           RADA_PYRFU   108 ATIGRISTGSKSLDKLLGGGIETQAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDTENTFRPERIREIAQNRGLDPDEVLKHIYVARAFNSNHQMLLVQQAEDKIKELLNTDRPVKLLIVDSLTSHFRSEYIGRGALAERQQKLAKHLADLHRLANLYDIAVFVTNQVQARPDAFFGDPTRPIGGHILAHSATLRVYLRKGKGGKRIARLIDAPHLPEGEAVFSITEKGIED 349
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee...hhhhhhhh...ee..eeeeeee....hhhhhhhhhhhhh..hhhhh....eeeeee.....hhhhhhhhhhh...hhhhhhhheeeee..hhhhhhhhhhhhhhhhhhhh.....eeeeeee..hhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.-----------------------..eeeeeee.hhh.eeeeee.------..eeeeee..eee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -RECA_2  PDB: A:109-285 UniProt: 109-285                                                                                                                                          ----RECA_3  PDB: A:309-349 UniProt: 290-349                      PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4b3d A 108 ATIGRISTGSKSLDKLLGGGIETQAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVMWIDTENTFRPERIREIAQNRGLDPDEVLKHIAYARAFNSNHQMLLVQQAEDMIKELLNTDRPVKLLIVDSLTSHFRSEYIGRGALAERQQKLAKHLADLHRLANLYDIAVFVTNQV-----------------------ATLRVYLRKGKGGKRIARLID------GEAVFSITEKGIED 349
                                   117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       | -         -         - |     317       327 |     337       347  
                                                                                                                                                                                                           285                     309                 329    336

Chain C from PDB  Type:PROTEIN  Length:215
 aligned with RADA_PYRFU | O74036 from UniProtKB/Swiss-Prot  Length:349

    Alignment length:242
                                   117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347  
           RADA_PYRFU   108 ATIGRISTGSKSLDKLLGGGIETQAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDTENTFRPERIREIAQNRGLDPDEVLKHIYVARAFNSNHQMLLVQQAEDKIKELLNTDRPVKLLIVDSLTSHFRSEYIGRGALAERQQKLAKHLADLHRLANLYDIAVFVTNQVQARPDAFFGDPTRPIGGHILAHSATLRVYLRKGKGGKRIARLIDAPHLPEGEAVFSITEKGIED 349
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee...hhhhhhhh...ee..eeeeeee....hhhhhhhhhhhhh..hhhhh....eeeeee.....hhhhhhhhhhhh..hhhhhhhheeeee..hhhhhhhhhhhhhhhhhhhh.....eeeeeee..hhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.----------------------...eeeeeee.hhh.eeeeee.-----...eeeeee..eee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -RECA_2  PDB: C:109-285 UniProt: 109-285                                                                                                                                          ----RECA_3  PDB: C:308-349 UniProt: 290-349                      PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4b3d C 108 ATIGRISTGSKSLDKLLGGGIETQAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVMWIDTENTFRPERIREIAQNRGLDPDEVLKHIAYARAFNSNHQMLLVQQAEDMIKELLNTDRPVKLLIVDSLTSHFRSEYIGRGALAERQQKLAKHLADLHRLANLYDIAVFVTNQV----------------------SATLRVYLRKGKGGKRIARLID-----EGEAVFSITEKGIED 349
                                   117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       | -         -         -|      317       327 |     337       347  
                                                                                                                                                                                                           285                    308                  329   335

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 4B3D)

(no "CATH Domain" information available for 4B3D)

(no "Pfam Domain" information available for 4B3D)

Asymmetric Unit(hide GO term definitions)

Chain A,C (RADA_PYRFU | O74036)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0008094	DNA-dependent ATPase activity	Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction requires the presence of single- or double-stranded DNA, and it drives another reaction.
	GO:0003684	damaged DNA binding	Interacting selectively and non-covalently with damaged DNA.
	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.
biological process
	GO:0006259	DNA metabolic process	Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides.
	GO:0006310	DNA recombination	Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.
	GO:0006281	DNA repair	The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
	GO:0006974	cellular response to DNA damage stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.

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	Cis Peptide Bonds
		Asp A:238 - Ser A:239	[ RasMol ]
		Asp C:238 - Ser C:239	[ RasMol ]

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	RADA_PYRFU \| O74036
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1pzn	RAD51 (RADA)
4a6p	RADA C-TERMINAL ATPASE DOMAIN FROM PYROCOCCUS FURIOSUS
4a6x	RADA C-TERMINAL ATPASE DOMAIN FROM PYROCOCCUS FURIOSUS BOUND TO ATP
4a74	RADA C-TERMINAL ATPASE DOMAIN FROM PYROCOCCUS FURIOSUS BOUND TO AMPPNP
4a7o	RADA C-TERMINAL ATPASE DOMAIN FROM PYROCOCCUS FURIOSUS BOUND TO ADP
4b2i	HUMANISED MONOMERIC RADA IN COMPLEX WITH INDAZOLE
4b2l	HUMANISED MONOMERIC RADA IN COMPLEX WITH L-METHYLESTER TRYPTOPHAN
4b2p	RADA C-TERMINAL ATPASE DOMAIN FROM PYROCOCCUS FURIOSUS BOUND TO GTP
4b32	HUMANISED MONOMERIC RADA IN COMPLEX WITH NAPHT-1-OL
4b33	HUMANISED MONOMERIC RADA IN COMPLEX WITH NAPHT-2-OL
4b34	HUMANISED MONOMERIC RADA IN COMPLEX WITH 2-AMINO BENZOTHIAZOLE
4b35	HUMANISED MONOMERIC RADA IN COMPLEX WITH 4-METHYLESTER INDOLE
4b3b	HUMANISED MONOMERIC RADA IN COMPLEX WITH FHTA TETRAPEPTIDE
4b3c	HUMANISED MONOMERIC RADA IN COMPLEX WITH 5-HYDROXY INDOLE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (0, 0)

CATH Domains (0, 0)

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Gene Ontology (9, 9)

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