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Description

Title :   CRYSTAL STRUCTURE OF APO-BRD4(1)

Authors :   D. Wohlwend

Date :   31 Jul 13 (Deposition) - 15 Jan 14 (Release) - 15 Jan 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.30

Chains :   Asym./Biol. Unit : A

Keywords :   Bromodomain, Epigenetic Reader Protein, Acetylated Lysin, Histone Tail, Nucleus, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   X. Lucas, D. Wohlwend, M. Hugle, K. Schmidtkunz, S. Gerhardt, R. Schule, M. Jung, O. Einsle, S. Gunther
4-Acyl Pyrroles: Mimicking Acetylated Lysines In Histone Code Reading.
Angew. Chem. Int. Ed. Engl. V. 52 14055 2013
PubMed-ID: 24272870 | Reference-DOI: 10.1002/ANIE.201307652

Compounds

Molecule 1 - BROMODOMAIN-CONTAINING PROTEIN 4
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PNIC28-BSA4
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	FIRST BROMODOMAIN DOMAIN (UNP RESIDUES 44-168)
	Gene	:	BRD4, HUNK1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	PROTEIN HUNK1

Structural Features

Chains, Units

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (4, 13)

Asymmetric/Biological Unit (4, 13)

No.	Name	Count	Type	Full Name
1	21H	1	Ligand/Ion	OXYDIMETHANOL
2	EDO	10	Ligand/Ion	1,2-ETHANEDIOL
3	IOD	1	Ligand/Ion	IODIDE ION
4	NA	1	Ligand/Ion	SODIUM ION

Sites (13, 13)

Asymmetric Unit (13, 13)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLY A:143 , VAL A:147 , GLU A:151 , HOH A:412	BINDING SITE FOR RESIDUE EDO A 201
02	AC2	SOFTWARE	LYS A:99 , LYS A:102 , EDO A:209 , HOH A:308 , HOH A:425	BINDING SITE FOR RESIDUE EDO A 202
03	AC3	SOFTWARE	ILE A:100 , ILE A:101 , LYS A:102 , THR A:103 , ASN A:135 , HOH A:450	BINDING SITE FOR RESIDUE EDO A 203
04	AC4	SOFTWARE	TRP A:75 , LYS A:76 , HIS A:77 , GLN A:84 , HOH A:343 , HOH A:385	BINDING SITE FOR RESIDUE EDO A 204
05	AC5	SOFTWARE	LYS A:155 , LEU A:158 , GLN A:159 , HOH A:384 , HOH A:410	BINDING SITE FOR RESIDUE EDO A 205
06	AC6	SOFTWARE	PRO A:82 , GLN A:85 , PRO A:86 , VAL A:87 , ASP A:88 , LEU A:92 , EDO A:207 , HOH A:457	BINDING SITE FOR RESIDUE EDO A 206
07	AC7	SOFTWARE	TRP A:81 , PRO A:82 , LEU A:92 , EDO A:206 , EDO A:208 , HOH A:371 , HOH A:436	BINDING SITE FOR RESIDUE EDO A 207
08	AC8	SOFTWARE	TRP A:81 , LYS A:99 , ILE A:146 , EDO A:207 , HOH A:425 , HOH A:453	BINDING SITE FOR RESIDUE EDO A 208
09	AC9	SOFTWARE	LYS A:57 , ARG A:58 , GLN A:59 , EDO A:202	BINDING SITE FOR RESIDUE EDO A 209
10	BC1	SOFTWARE	GLN A:59 , GLN A:64 , ARG A:68 , HOH A:365 , HOH A:434	BINDING SITE FOR RESIDUE EDO A 210
11	BC2	SOFTWARE	GLN A:64	BINDING SITE FOR RESIDUE IOD A 211
12	BC3	SOFTWARE	TYR A:137 , ILE A:138 , ASN A:140 , GLU A:163 , 21H A:213 , HOH A:469	BINDING SITE FOR RESIDUE NA A 212
13	BC4	SOFTWARE	THR A:134 , TYR A:137 , LYS A:160 , GLU A:163 , NA A:212 , HOH A:403	BINDING SITE FOR RESIDUE 21H A 213

SS Bonds (0, 0)

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

Cis Peptide Bonds (0, 0)

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

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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

PROSITE Motifs (0, 0)

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

Exons (0, 0)

(no "Exon" information available for 4LYI)

Sequences/Alignments

Asymmetric/Biological 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:127
                                                                                                                                                               
               SCOP domains d4lyia_ A: automated matches                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................hhhhhhhhhhhhhhhhh...hhhhh...........hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lyi A  42 SMNPPPPETSNPNKPKRQTNQLQYLLRVVLKTLWKHQFAWPFQQPVDAVKLNLPDYYKIIKTPMDMGTIKKRLENNYYWNAQECIQDFNTMFTNCYIYNKPGDDIVLMAEALEKLFLQKINELPTEE 168
                                    51        61        71        81        91       101       111       121       131       141       151       161

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: Bromodomain-like (339)

Superfamily: Bromodomain (203)

Family: automated matches (169)

Protein domain: automated matches (169)

Human (Homo sapiens) [TaxId: 9606] (162)

d4lyia_

CATH Domains (0, 0)

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

Pfam Domains (0, 0)

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

Gene Ontology (22, 22)

Asymmetric/Biological Unit(hide GO term definitions)

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	Cis Peptide Bonds
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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
	BRD4_HUMAN \| O60885	:	2i8n 2lsp 2mjv 2n3k 2ncz 2nd0 2nd1 2nnu 2oss 2ouo 2yel 2yem 3mxf 3p5o 3svf 3svg 3u5j 3u5k 3u5l 3uvw 3uvx 3uvy 3uw9 3zyu 4a9l 4bjx 4bw1 4bw2 4bw3 4bw4 4c66 4c67 4cfk 4cfl 4cl9 4clb 4don 4e96 4f3i 4gpj 4hbv 4hbw 4hbx 4hby 4hxk 4hxl 4hxm 4hxn 4hxo 4hxp 4hxr 4hxs 4ioo 4ioq 4ior 4j0r 4j0s 4j3i 4kv1 4kv4 4lr6 4lrg 4lys 4lyw 4lzr 4lzs 4men 4meo 4mep 4meq 4mr3 4mr4 4nqm 4nr8 4nuc 4nud 4nue 4o70 4o71 4o72 4o74 4o75 4o76 4o77 4o78 4o7a 4o7b 4o7c 4o7e 4o7f 4ogi 4ogj 4pce 4pci 4ps5 4qb3 4qr3 4qr4 4qr5 4qzs 4uix 4uiy 4uiz 4uyd 4whw 4wiv 4x2i 4xy9 4xya 4yh3 4yh4 4z1q 4z1s 4z93 4zc9 4zw1 5a5s 5a85 5acy 5ad2 5ad3 5bt4 5cfw 5coi 5cp5 5cpe 5cqt 5crm 5crz 5cs8 5ctl 5cy9 5d0c 5d24 5d25 5d26 5d3h 5d3j 5d3l 5d3n 5d3p 5d3r 5d3s 5d3t 5dlx 5dlz 5dw2 5dx4 5e0r 5egu 5ei4 5eis 5f5z 5f60 5f61 5f62 5f63 5fbx 5h21 5hcl 5hls 5hm0 5hq5 5hq6 5hq7 5i80 5i88 5igk 5jwm 5khm 5ku3 5lj1 5lj2 5luu 5t35 5u28 5u2c 5u2e 5u2f 5ueo 5uep 5ueq 5uer 5ues 5uet 5ueu 5uev 5uex 5uey 5uez 5uf0 5ula 5uoo 5uvs 5uvt 5uvu 5uvv 5uvw 5uvx 5uvy 5uvz 5wuu

Related Entries Specified in the PDB File

4lys 4lyw 4lzr 4lzs