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Description

Title :   CRYSTAL STRUCTURE OF HUMAN CBR1 IN COMPLEX WITH HYDROXY-PP

Authors :   D. Rauh, R. Bateman, K. M. Shokat

Date :   06 Jul 04 (Deposition) - 26 Apr 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.24

Chains :   Asym./Biol. Unit : A

Keywords :   Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Tanaka, R. Bateman, D. Rauh, E. Vaisberg, S. Ramachandani, C. Zhang, K. C. Hansen, A. L. Burlingame, J. K. Trautman, K. M. Shokat, C. L. Adams
An Unbiased Cell Morphology-Based Screen For New, Biologically Active Small Molecules
Plos Biol. V. 3 128 2005
PubMed-ID: 15799708 | Reference-DOI: 10.1371/JOURNAL.PBIO.0030128
(for further references see the PDB file header)

Compounds

Molecule 1 - CARBONYL REDUCTASE [NADPH] 1
	Chains	:	A
	EC Number	:	1.1.1.184
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET-11A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Structural Features

Chains, Units

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (5, 12)

Asymmetric/Biological Unit (5, 12)

No.	Name	Count	Type	Full Name
1	AB3	2	Ligand/Ion	3-(4-AMINO-1-TERT-BUTYL-1H-PYRAZOLO[3,4-D]PYRIMIDIN-3-YL)PHENOL
2	NDP	1	Ligand/Ion	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
3	P33	1	Ligand/Ion	3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL
4	PE5	1	Ligand/Ion	3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL
5	SO4	7	Ligand/Ion	SULFATE ION

Sites (12, 12)

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ARG A:57 , PHE A:58 , HOH A:542 , HOH A:639	BINDING SITE FOR RESIDUE SO4 A 300
02	AC2	SOFTWARE	PHE A:102 , SER A:190 , SER A:191 , ALA A:192 , TYR A:193 , SO4 A:305 , HOH A:424 , HOH A:458 , HOH A:553 , HOH A:559	BINDING SITE FOR RESIDUE SO4 A 301
03	AC3	SOFTWARE	LYS A:216 , GLY A:217 , ASP A:218 , LYS A:219 , HOH A:506 , HOH A:511 , HOH A:761	BINDING SITE FOR RESIDUE SO4 A 302
04	AC4	SOFTWARE	ASP A:64 , LYS A:111 , THR A:163 , ARG A:209 , LYS A:210 , GLU A:213 , HOH A:446 , HOH A:460 , HOH A:677	BINDING SITE FOR RESIDUE SO4 A 303
05	AC5	SOFTWARE	ARG A:41 , ARG A:118 , HOH A:571 , HOH A:656 , HOH A:675 , HOH A:684	BINDING SITE FOR RESIDUE SO4 A 304
06	AC6	SOFTWARE	VAL A:96 , ALA A:97 , ARG A:272 , SO4 A:301 , HOH A:502 , HOH A:553 , HOH A:559 , HOH A:576	BINDING SITE FOR RESIDUE SO4 A 305
07	AC7	SOFTWARE	SER A:2 , GLY A:3 , GLN A:47 , GLN A:50 , LYS A:129 , HOH A:742	BINDING SITE FOR RESIDUE SO4 A 306
08	AC8	SOFTWARE	SER A:139 , MET A:141 , TYR A:193 , GLY A:228 , TRP A:229 , AB3 A:308 , NDP A:309 , PE5 A:310 , HOH A:479	BINDING SITE FOR RESIDUE AB3 A 307
09	AC9	SOFTWARE	ARG A:22 , ARG A:26 , ILE A:140 , ARG A:144 , GLU A:244 , AB3 A:307 , PE5 A:310 , HOH A:484 , HOH A:607 , HOH A:642	BINDING SITE FOR RESIDUE AB3 A 308
10	BC1	SOFTWARE	GLY A:11 , ASN A:13 , LYS A:14 , GLY A:15 , ILE A:16 , ARG A:37 , LEU A:61 , ASP A:62 , ILE A:63 , ASP A:64 , ASN A:89 , ALA A:90 , GLY A:91 , ILE A:92 , VAL A:137 , SER A:138 , TYR A:193 , LYS A:197 , PRO A:227 , GLY A:228 , TRP A:229 , VAL A:230 , THR A:232 , ASP A:233 , MET A:234 , ALA A:235 , AB3 A:307 , HOH A:402 , HOH A:406 , HOH A:407 , HOH A:430 , HOH A:449 , HOH A:481 , HOH A:523 , HOH A:549 , HOH A:661 , HOH A:664 , HOH A:666 , HOH A:721	BINDING SITE FOR RESIDUE NDP A 309
11	BC2	SOFTWARE	ASP A:23 , ALA A:93 , MET A:141 , ARG A:144 , MET A:234 , GLU A:248 , TYR A:252 , AB3 A:307 , AB3 A:308 , HOH A:416 , HOH A:423 , HOH A:466 , HOH A:495	BINDING SITE FOR RESIDUE PE5 A 310
12	BC3	SOFTWARE	ALA A:93 , THR A:122 , LEU A:125 , HIS A:207 , LYS A:210 , LEU A:211 , GLN A:214 , HOH A:623 , HOH A:697 , HOH A:730	BINDING SITE FOR RESIDUE P33 A 311

SS Bonds (0, 0)

(no "SS Bond" information available for 1WMA)

Cis Peptide Bonds (1, 1)

Asymmetric/Biological Unit

No.	Residues
1	Gly A:262	-	Pro A:263

Sequence-Structure Mapping

SAPs(SNPs)/Variants (2, 2)

Asymmetric/Biological Unit (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_059053	V	88	I	CBR1_HUMAN	Polymorphism	1143663	A	V	87	I
2	UniProt	VAR_031706	P	131	S	CBR1_HUMAN	Polymorphism	41557318	A	P	130	S

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

PROSITE Motifs (1, 1)

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADH_SHORT	PS00061	Short-chain dehydrogenases/reductases family signature.	CBR1_HUMAN	181-209	1	A:180-208

Exons (3, 3)

Asymmetric/Biological Unit (3, 3)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000290349	1a	ENSE00002172104	chr21:37442239-37442702	464	CBR1_HUMAN	1-97	97	1	A:2-96	95
1.2a	ENST00000290349	2a	ENSE00001044165	chr21:37443248-37443355	108	CBR1_HUMAN	97-133	37	1	A:96-132	37
1.3c	ENST00000290349	3c	ENSE00001044162	chr21:37444744-37445464	721	CBR1_HUMAN	133-277	145	1	A:132-276	145

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
	(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:275
 aligned with CBR1_HUMAN | P16152 from UniProtKB/Swiss-Prot  Length:277

    Alignment length:275
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272     
           CBR1_HUMAN     3 SGIHVALVTGGNKGIGLAIVRDLCRLFSGDVVLTARDVTRGQAAVQQLQAEGLSPRFHQLDIDDLQSIRALRDFLRKEYGGLDVLVNNAGIAFKVADPTPFHIQAEVTMKTNFFGTRDVCTELLPLIKPQGRVVNVSSIMSVRALKSCSPELQQKFRSETITEEELVGLMNKFVEDTKKGVHQKEGWPSSAYGVTKIGVTVLSRIHARKLSEQRKGDKILLNACCPGWVRTDMAGPKATKSPEEGAETPVYLALLPPDAEGPHGQFVSEKRVEQW 277
               SCOP domains d1wmaa1 A:2-276 Carbonyl reductase/20beta-hydroxysteroid dehydrogenase                                                                                                                                                                                                              SCOP domains
               CATH domains 1wmaA00 A:2-276 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                                                 CATH domains
               Pfam domains ---adh_short-1wmaA01 A:5-150                                                                                                                         ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeee....hhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhhhh.eeeeee............hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeee.hhhhhhhhhh.hhhhhhhhhh...hhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeee...............hhhhhhhhhhhhhh...........eee..eee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------I------------------------------------------S-------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: A:180-208    -------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a  PDB: A:2-96 UniProt: 1-97 [INCOMPLETE]                                              -----------------------------------Exon 1.3c  PDB: A:132-276 UniProt: 133-277                                                                                                        Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------------------Exon 1.2a  PDB: A:96-132             ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript 1 (2)
                 1wma A   2 SGIHVALVTGGNKGIGLAIVRDLCRLFSGDVVLTARDVTRGQAAVQQLQAEGLSPRFHQLDIDDLQSIRALRDFLRKEYGGLDVLVNNAGIAFKVADPTPFHIQAEVTMKTNFFGTRDVCTELLPLIKPQGRVVNVSSIMSVRALKSCSPELQQKFRSETITEEELVGLMNKFVEDTKKGVHQKEGWPSSAYGVTKIGVTVLSRIHARKLSEQRKGDKILLNACCPGWVRTDMAGPKATKSPEEGAETPVYLALLPPDAEGPHGQFVSEKRVEQW 276
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271

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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: NAD(P)-binding Rossmann-fold domains (1604)

Superfamily: NAD(P)-binding Rossmann-fold domains (1604)

Family: Tyrosine-dependent oxidoreductases (503)

Protein domain: Carbonyl reductase/20beta-hydroxysteroid dehydrogenase (6)

Human (Homo sapiens) [TaxId: 9606] (5)

d1wmaa1

A:2-276

CATH Domains (1, 1)

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: NAD(P)-binding Rossmann-like Domain (1244)

Human (Homo sapiens) (188)

1wmaA00

A:2-276

Pfam Domains (1, 1)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: NADP_Rossmann (1239)

Family: adh_short (92)

Homo sapiens (Human) (21)

adh_short-1wmaA01

A:5-150

Gene Ontology (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (CBR1_HUMAN | P16152)

molecular function
	GO:0047021	15-hydroxyprostaglandin dehydrogenase (NADP+) activity	Catalysis of the reaction: NADP(+) + prostaglandin E(1) = 15-dehydro-prostaglandin E1 + H(+) + NADPH.
	GO:0004090	carbonyl reductase (NADPH) activity	Catalysis of the reaction: R-CHOH-R' + NADP+ = R-CO-R' + NADPH + H+.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	GO:0016655	oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor	Catalysis of an oxidation-reduction (redox) reaction in which NADH or NADPH acts as a hydrogen or electron donor and reduces a quinone or a similar acceptor molecule.
	GO:0050221	prostaglandin-E2 9-reductase activity	Catalysis of the reaction: (5Z,13E)-(15S)-9-alpha,11-alpha,15-trihydroxyprosta-5,13-dienoate + NADP+ = (5Z,13E)-(15S)-11-alpha,15-dihydroxy-9-oxoprosta-5,13-dienoate + NADPH.
biological process
	GO:0019371	cyclooxygenase pathway	The chemical reactions and pathways by which prostaglandins are formed from arachidonic acid, and in which prostaglandin-endoperoxide synthase (cyclooxygenase) catalyzes the committed step in the conversion of arachidonic acid to the prostaglandin-endoperoxides PGG2 and PGH2.
	GO:0017144	drug metabolic process	The chemical reactions and pathways involving a drug, a substance used in the diagnosis, treatment or prevention of a disease; as used here antibiotic substances (see antibiotic metabolism) are considered to be drugs, even if not used in medical or veterinary practice.
	GO:0030855	epithelial cell differentiation	The process in which a relatively unspecialized cell acquires specialized features of an epithelial cell, any of the cells making up an epithelium.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	GO:0042373	vitamin K metabolic process	The chemical reactions and pathways involving any of the forms of vitamin K, quinone-derived vitamins which are involved in the synthesis of blood-clotting factors in mammals. Vitamin K substances share a methylated naphthoquinone ring structure and vary in the aliphatic side chains attached to the molecule.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:1903561	extracellular vesicle	Any vesicle that is part of the extracellular region.

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	Cis Peptide Bonds
		Gly A:262 - Pro A:263	[ RasMol ]

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
	CBR1_HUMAN \| P16152	:	2pfg 3bhi 3bhj 3bhm 4z3d

Related Entries Specified in the PDB File

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