5DW1 - JenaLib

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Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   X-RAY CRYSTAL STRUCTURE OF HUMAN BRD2(BD2) IN COMPLEX WITH RVX297 TO 1.55 A RESOLUTION

Authors :   A. White, E. Fontano, R. K. Suto

Date :   22 Sep 15 (Deposition) - 22 Jun 16 (Release) - 20 Jul 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.55

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

Keywords :   Bromodomain, Protein Binding-Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   O. A. Kharenko, E. M. Gesner, R. G. Patel, K. Norek, A. White, E. Fontano R. K. Suto, P. R. Young, K. G. Mclure, H. C. Hansen
Rvx-297- A Novel Bd2 Selective Inhibitor Of Bet Bromodomains.
Biochem. Biophys. Res. Commun. V. 477 62 2016
PubMed-ID: 27282480 | Reference-DOI: 10.1016/J.BBRC.2016.06.021

Molecule 1 - BROMODOMAIN-CONTAINING PROTEIN 2
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PJEXPRESS401
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	BD2 (UNP RESIDUES 345-455)
	Gene	:	BRD2, KIAA9001, RING3
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	O27.1.1, REALLY INTERESTING NEW GENE 3 PROTEIN

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 6)

No.	Name	Count	Type	Full Name
1	5GD	4	Ligand/Ion	2-{3,5-DIMETHYL-4-[2-(PYRROLIDIN-1-YL)ETHOXY]PHENYL}-5,7-DIMETHOXYQUINAZOLIN-4(3H)-ONE
2	NA	2	Ligand/Ion	SODIUM ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	5GD	1	Ligand/Ion	2-{3,5-DIMETHYL-4-[2-(PYRROLIDIN-1-YL)ETHOXY]PHENYL}-5,7-DIMETHOXYQUINAZOLIN-4(3H)-ONE
2	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	5GD	1	Ligand/Ion	2-{3,5-DIMETHYL-4-[2-(PYRROLIDIN-1-YL)ETHOXY]PHENYL}-5,7-DIMETHOXYQUINAZOLIN-4(3H)-ONE
2	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	5GD	1	Ligand/Ion	2-{3,5-DIMETHYL-4-[2-(PYRROLIDIN-1-YL)ETHOXY]PHENYL}-5,7-DIMETHOXYQUINAZOLIN-4(3H)-ONE
2	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 4 (1, 1)

No.	Name	Count	Type	Full Name
1	5GD	1	Ligand/Ion	2-{3,5-DIMETHYL-4-[2-(PYRROLIDIN-1-YL)ETHOXY]PHENYL}-5,7-DIMETHOXYQUINAZOLIN-4(3H)-ONE
2	NA	-1	Ligand/Ion	SODIUM ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TRP A:370 , PRO A:371 , PHE A:372 , VAL A:376 , LEU A:381 , LEU A:383 , ASN A:429 , HIS A:433 , HOH A:626 , HOH D:636	binding site for residue 5GD A 500
2	AC2	SOFTWARE	PRO B:371 , PHE B:372 , VAL B:376 , LEU B:381 , LEU B:383 , ASN B:429 , HIS B:433 , VAL B:435 , HOH B:616 , HOH B:630 , HOH C:629 , HOH C:643 , HOH C:689	binding site for residue 5GD B 500
3	AC3	SOFTWARE	TRP B:370 , ALA B:380 , TRP C:370 , PRO C:371 , PHE C:372 , VAL C:376 , LEU C:381 , ASN C:429 , HIS C:433 , HOH C:625 , HOH C:651 , HOH C:672 , HOH C:690 , HIS D:384	binding site for residue 5GD C 501
4	AC4	SOFTWARE	ASP C:377 , SER C:379 , HOH C:679 , HOH C:712 , HOH C:719	binding site for residue NA C 502
5	AC5	SOFTWARE	TRP A:370 , ALA A:380 , SER B:379 , HIS B:384 , PRO D:371 , PHE D:372 , VAL D:376 , LEU D:381 , LEU D:383 , ASN D:429 , HIS D:433 , HOH D:630 , HOH D:678 , HOH D:701	binding site for residue 5GD D 501
6	AC6	SOFTWARE	HOH A:661 , HOH A:671 , HOH A:699 , HOH B:646 , GLY D:382 , HOH D:683	binding site for residue NA D 502

(no "SS Bond" information available for 5DW1)

(no "Cis Peptide Bond" information available for 5DW1)

(no "SAP(SNP)/Variant" information available for 5DW1)

(no "PROSITE Motif" information available for 5DW1)

(no "Exon" information available for 5DW1)

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
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Chain A from PDB  Type:PROTEIN  Length:111
                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh..hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                 5dw1 A 345 KLSEQLKHCNGILKELLSKKHAAYAWPFYKPVDASALGLHDYHDIIKHPMDLSTVKRKMENRDYRDAQEFAADVRLMFSNCYKYNPPDHDVVAMARKLQDVFEFRYAKMPD 455
                                   354       364       374       384       394       404       414       424       434       444       454

Chain B from PDB  Type:PROTEIN  Length:110
                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh..hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 5dw1 B 346 LSEQLKHCNGILKELLSKKHAAYAWPFYKPVDASALGLHDYHDIIKHPMDLSTVKRKMENRDYRDAQEFAADVRLMFSNCYKYNPPDHDVVAMARKLQDVFEFRYAKMPD 455
                                   355       365       375       385       395       405       415       425       435       445       455

Chain C from PDB  Type:PROTEIN  Length:110
                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 5dw1 C 346 LSEQLKHCNGILKELLSKKHAAYAWPFYKPVDASALGLHDYHDIIKHPMDLSTVKRKMENRDYRDAQEFAADVRLMFSNCYKYNPPDHDVVAMARKLQDVFEFRYAKMPD 455
                                   355       365       375       385       395       405       415       425       435       445       455

Chain D from PDB  Type:PROTEIN  Length:110
                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh..hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 5dw1 D 346 LSEQLKHCNGILKELLSKKHAAYAWPFYKPVDASALGLHDYHDIIKHPMDLSTVKRKMENRDYRDAQEFAADVRLMFSNCYKYNPPDHDVVAMARKLQDVFEFRYAKMPD 455
                                   355       365       375       385       395       405       415       425       435       445       455

Legend:		→ Mismatch	(orange background)
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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 '\|'

(no "SCOP Domain" information available for 5DW1)

(no "CATH Domain" information available for 5DW1)

(no "Pfam Domain" information available for 5DW1)

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Description

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Chains, Units

Ligands, Modified Residues, Ions (2, 6)

Sites (6, 6)

SS Bonds (0, 0)

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