2PFG - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HUMAN CBR1 IN COMPLEX WITH BIGF2.

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

Date :   04 Apr 07 (Deposition) - 25 Sep 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.54

Chains :   Asym./Biol. Unit : A

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

Reference :   R. Bateman, D. Rauh, K. M. Shokat
Glutathione Traps Formaldehyde By Formation Of A Bicyclo[4. 4. 1]Undecane Adduct.
Org. Biomol. Chem. V. 5 3363 2007
PubMed-ID: 17912391 | Reference-DOI: 10.1039/B707602A

Molecule 1 - CARBONYL REDUCTASE [NADPH] 1
	Chains	:	A
	EC Number	:	1.1.1.184, 1.1.1.189, 1.1.1.197
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET11B
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	CBR1, CBR, CRN
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	NADPH-DEPENDENT CARBONYL REDUCTASE 1, PROSTAGLANDIN-E2, 9- REDUCTASE, PROSTAGLANDIN 9-KETOREDUCTASE, 15-HYDROXYPROSTAGLANDIN DEHYDROGENASE [NADP+]

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (5, 5)

No.	Name	Count	Type	Full Name
1	CL	1	Ligand/Ion	CHLORIDE ION
2	DDD	1	Ligand/Ion	(5R,10S)-5-{[(CARBOXYMETHYL)AMINO]CARBONYL}-7-OXO-3-THIA-1,6-DIAZABICYCLO[4.4.1]UNDECANE-10-CARBOXYLICACID
3	GOL	1	Ligand/Ion	GLYCEROL
4	M0H	1	Mod. Amino Acid	S-(HYDROXYMETHYL)-L-CYSTEINE
5	NAP	1	Ligand/Ion	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

(no "Site" information available for 2PFG)

(no "SS Bond" information available for 2PFG)

Asymmetric/Biological Unit

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

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)

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

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:3-96	94
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

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:274
 aligned with CBR1_HUMAN | P16152 from UniProtKB/Swiss-Prot  Length:277

    Alignment length:274
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273    
           CBR1_HUMAN     4 GIHVALVTGGNKGIGLAIVRDLCRLFSGDVVLTARDVTRGQAAVQQLQAEGLSPRFHQLDIDDLQSIRALRDFLRKEYGGLDVLVNNAGIAFKVADPTPFHIQAEVTMKTNFFGTRDVCTELLPLIKPQGRVVNVSSIMSVRALKSCSPELQQKFRSETITEEELVGLMNKFVEDTKKGVHQKEGWPSSAYGVTKIGVTVLSRIHARKLSEQRKGDKILLNACCPGWVRTDMAGPKATKSPEEGAETPVYLALLPPDAEGPHGQFVSEKRVEQW 277
               SCOP domains d2pfga_ A: Carbonyl reductase/20beta-hydroxysteroid dehydrogenase                                                                                                                                                                                                                  SCOP domains
               CATH domains 2pfgA00 A:3-276 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                                                CATH domains
               Pfam domains --adh_short-2pfgA01 A:5-150                                                                                                                         ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee....hhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhh.....eeee....hhhhhhhhhhhhhhhhh.eeeeee............hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeee..hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.........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:3-96 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)
                 2pfg A   3 GIHVALVTGGNKGIGLAIVRDLCRLFSGDVVLTARDVTRGQAAVQQLQAEGLSPRFHQLDIDDLQSIRALRDFLRKEYGGLDVLVNNAGIAFKVADPTPFHIQAEVTMKTNFFGTRDVcTELLPLIKPQGRVVNVSSIMSVRALKSCSPELQQKFRSETITEEELVGLMNKFVEDTKKGVHQKEGWPSSAYGVTKIGVTVLSRIHARKLSEQRKGDKILLNACCPGWVRTDMAGPKATKSPEEGAETPVYLALLPPDAEGPHGQFVSEKRVEQW 276
                                    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    
                                                                                                                                                121-M0H

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 '\|'

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)

d2pfga_

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)

2pfgA00

A:3-276

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: NADP_Rossmann (1239)

Family: adh_short (92)

Homo sapiens (Human) (21)

adh_short-2pfgA01

A:5-150

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.

Asymmetric/Biological Unit
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	Sites
(no "Sites" information available for 2pfg)

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

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	2pfg
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	CBR1_HUMAN \| P16152
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	1.1.1.184
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	1.1.1.189
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	1.1.1.197
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	CBR1_HUMAN \| P16152
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	CBR1_HUMAN \| P16152	:	1wma 3bhi 3bhj 3bhm 4z3d

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 5)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (2, 2)

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Exons (3, 3)

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