2YAN - JenaLib

Title :   CRYSTAL STRUCTURE OF THE SECOND GLUTAREDOXIN DOMAIN OF HUMAN TXNL2

Authors :   M. Vollmar, C. Johansson, R. Cocking, J. R. C. Muniz, T. Krojer, C. Aller F. Von Delft, C. Bountra, C. H. Arrowsmith, J. Weigelt, A. Edwards, U. Oppermann

Date :   23 Feb 11 (Deposition) - 30 Nov 11 (Release) - 05 Dec 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

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

Reference :   M. Vollmar, C. Johansson, R. Cocking, J. R. C. Muniz, T. Krojer, C. Allerston, F. Von Delft, C. Bountra, C. H. Arrowsmith, J. Weigelt, A. Edwards, U. Oppermann
Crystal Structure Of The Second Glutaredoxin Domain Of Human Txnl2
To Be Published
PubMed: search

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 12)

Sites (12, 12)

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	LYS A:319 , GLU A:323 , HOH A:2093	BINDING SITE FOR RESIDUE EDO A1334
02	AC2	SOFTWARE	LYS A:294 , ASN A:298 , TRP A:299 , EDO B:1335	BINDING SITE FOR RESIDUE EDO A1335
03	AC3	SOFTWARE	CYS A:261 , GSH A:1341 , HOH A:2094 , HOH A:2095 , HOH A:2096 , GLN B:257	BINDING SITE FOR RESIDUE EDO A1336
04	AC4	SOFTWARE	LYS A:256 , GLU A:279 , THR A:280 , HOH A:2045	BINDING SITE FOR RESIDUE EDO A1337
05	AC5	SOFTWARE	GSH A:1341 , HOH A:2023	BINDING SITE FOR RESIDUE FE A1338
06	AC6	SOFTWARE	LYS A:253 , LYS A:260 , ARG A:290	BINDING SITE FOR RESIDUE SO4 A1339
07	AC7	SOFTWARE	GLY A:314 , ASP A:316 , ILE A:317 , GSH A:1341	BINDING SITE FOR RESIDUE CL A1340
08	AC8	SOFTWARE	LYS A:253 , CYS A:261 , PHE A:263 , ARG A:290 , LYS A:294 , THR A:301 , TYR A:302 , PRO A:303 , GLY A:314 , LEU A:315 , ASP A:316 , EDO A:1336 , FE A:1338 , CL A:1340 , HOH A:2065 , HOH A:2097 , GLN B:257	BINDING SITE FOR RESIDUE GSH A1341
09	AC9	SOFTWARE	ASN A:298 , EDO A:1335 , LYS B:256 , GLU B:279 , THR B:280 , HOH B:2042 , HOH B:2043	BINDING SITE FOR RESIDUE EDO B1335
10	BC1	SOFTWARE	LEU A:321 , GLU A:326 , GLN B:266 , GLU B:269 , LYS B:319	BINDING SITE FOR RESIDUE EDO B1336
11	BC2	SOFTWARE	GLU A:320 , GLY B:262 , GSH B:1338	BINDING SITE FOR RESIDUE EDO B1337
12	BC3	SOFTWARE	LYS B:253 , LYS B:260 , CYS B:261 , ARG B:290 , EDO B:1337 , HOH B:2026	BINDING SITE FOR RESIDUE GSH B1338

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (6, 12)

Asymmetric Unit (6, 12)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000368644	1	ENSE00002174390	chr10:131934663-131934776	114	GLRX3_HUMAN	1-31	31	0	-	-
1.2	ENST00000368644	2	ENSE00000728668	chr10:131943475-131943583	109	GLRX3_HUMAN	31-67	37	0	-	-
1.4	ENST00000368644	4	ENSE00000728671	chr10:131958259-131958333	75	GLRX3_HUMAN	68-92	25	0	-	-
1.5b	ENST00000368644	5b	ENSE00000728676	chr10:131959060-131959261	202	GLRX3_HUMAN	93-160	68	0	-	-
1.6	ENST00000368644	6	ENSE00000728678	chr10:131964771-131964943	173	GLRX3_HUMAN	160-217	58	0	-	-
1.7	ENST00000368644	7	ENSE00000728681	chr10:131965183-131965244	62	GLRX3_HUMAN	218-238	21	2	A:230-238 B:230-238	9 9
1.8	ENST00000368644	8	ENSE00000728683	chr10:131967697-131967754	58	GLRX3_HUMAN	238-257	20	2	A:238-257 B:238-257	20 20
1.9	ENST00000368644	9	ENSE00000728687	chr10:131969848-131969900	53	GLRX3_HUMAN	258-275	18	2	A:258-275 B:258-275	18 18
1.10	ENST00000368644	10	ENSE00000728691	chr10:131973131-131973170	40	GLRX3_HUMAN	275-288	14	2	A:275-288 B:275-288	14 14
1.11	ENST00000368644	11	ENSE00000577957	chr10:131973261-131973353	93	GLRX3_HUMAN	289-319	31	2	A:289-319 B:289-319	31 31
1.12a	ENST00000368644	12a	ENSE00001217321	chr10:131977606-131977684	79	GLRX3_HUMAN	320-335	16	2	A:320-334 B:320-334	15 15
1.13b	ENST00000368644	13b	ENSE00001217252	chr10:131978377-131978640	264	GLRX3_HUMAN	-	0	0	-	-

Sequences/Alignments

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:105
 aligned with GLRX3_HUMAN | O76003 from UniProtKB/Swiss-Prot  Length:335

    Alignment length:105
                                   239       249       259       269       279       289       299       309       319       329     
          GLRX3_HUMAN   230 PKAPKLEERLKVLTNKASVMLFMKGNKQEAKCGFSKQILEILNSTGVEYETFDILEDEEVRQGLKAYSNWPTYPQLYVKGELVGGLDIVKELKENGELLPILRGE 334
               SCOP domains d2yana_ A: automated matches                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh...eeeee.........hhhhhhhhhhhhh....eeee...hhhhhhhhhhhhh.....eeee..eeeehhhhhhhhhhh.hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) GLUTARE-------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ------GLUTAREDOXIN_2  PDB: A:236-334 UniProt: 236-335                                                     PROSITE (2)
           Transcript 1 (1) Exon 1.7 ------------------------------------Exon 1.10     Exon 1.11  PDB: A:289-319      Exon 1.12a      Transcript 1 (1)
           Transcript 1 (2) --------Exon 1.8            Exon 1.9          ----------------------------------------------------------- Transcript 1 (2)
                 2yan A 230 SMAPKLEERLKVLTNKASVMLFMKGNKQEAKCGFSKQILEILNSTGVEYETFDILEDEEVRQGLKAYSNWPTYPQLYVKGELVGGLDIVKELKENGELLPILRGE 334
                                   239       249       259       269       279       289       299       309       319       329

Chain B from PDB  Type:PROTEIN  Length:105
 aligned with GLRX3_HUMAN | O76003 from UniProtKB/Swiss-Prot  Length:335

    Alignment length:105
                                   239       249       259       269       279       289       299       309       319       329     
          GLRX3_HUMAN   230 PKAPKLEERLKVLTNKASVMLFMKGNKQEAKCGFSKQILEILNSTGVEYETFDILEDEEVRQGLKAYSNWPTYPQLYVKGELVGGLDIVKELKENGELLPILRGE 334
               SCOP domains d2yanb_ B: automated matches                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh...eeeee........hhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhh.....eeee..eeeehhhhhhhhhhh.hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) GLUTARE-------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ------GLUTAREDOXIN_2  PDB: B:236-334 UniProt: 236-335                                                     PROSITE (2)
           Transcript 1 (1) Exon 1.7 ------------------------------------Exon 1.10     Exon 1.11  PDB: B:289-319      Exon 1.12a      Transcript 1 (1)
           Transcript 1 (2) --------Exon 1.8            Exon 1.9          ----------------------------------------------------------- Transcript 1 (2)
                 2yan B 230 SMAPKLEERLKVLTNKASVMLFMKGNKQEAKCGFSKQILEILNSTGVEYETFDILEDEEVRQGLKAYSNWPTYPQLYVKGELVGGLDIVKELKENGELLPILRGE 334
                                   239       249       259       269       279       289       299       309       319       329

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, 2)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (16, 16)

Asymmetric Unit(hide GO term definitions)

Chain A,B (GLRX3_HUMAN | O76003)

molecular function
	GO:0009055	electron carrier activity	Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
	GO:0051536	iron-sulfur cluster binding	Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0015035	protein disulfide oxidoreductase activity	Catalysis of the reaction: a protein with reduced sulfide groups = a protein with oxidized disulfide bonds.
	GO:0005080	protein kinase C binding	Interacting selectively and non-covalently with protein kinase C.
biological process
	GO:0045454	cell redox homeostasis	Any process that maintains the redox environment of a cell or compartment within a cell.
	GO:0010614	negative regulation of cardiac muscle hypertrophy	Any process that decreases the rate, frequency or extent of the enlargement or overgrowth of all or part of the heart due to an increase in size (not length) of individual cardiac muscle fibers, without cell division.
	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:0002026	regulation of the force of heart contraction	Any process that modulates the extent of heart contraction, changing the force with which blood is propelled.
cellular component
	GO:0030018	Z disc	Platelike region of a muscle sarcomere to which the plus ends of actin filaments are attached.
	GO:0005938	cell cortex	The region of a cell that lies just beneath the plasma membrane and often, but not always, contains a network of actin filaments and associated proteins.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0030425	dendrite	A neuron projection that has a short, tapering, often branched, morphology, receives and integrates signals from other neurons or from sensory stimuli, and conducts a nerve impulse towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body.
	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:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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