3B6P - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   STRUCTURE OF TREX1 IN COMPLEX WITH A NUCLEOTIDE AND INHIBITOR IONS (SODIUM AND ZINC)

Authors :   M. Brucet, J. Querol-Audi, I. Fita, A. Celada

Date :   29 Oct 07 (Deposition) - 23 Sep 08 (Release) - 09 Jun 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Trex1, Dedd, Exonuclease, Dnaq, Sodium, Zinc, Catalysis, Inhibition, Deoxy-Thimidine Monophosphate (Dtmp), Dna Damage, Dna Repair, Hydrolase, Magnesium, Nucleus, Phosphorylation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Brucet, J. Querol-Audi, K. Bertlik, J. Lloberas, I. Fita, A. Celada
Structural And Biochemical Studies Of Trex1 Inhibition By Metals. Identification Of A New Active Histidine Conserved In Deddh Exonucleases.
Protein Sci. V. 17 2059 2008
PubMed-ID: 18780819 | Reference-DOI: 10.1110/PS.036426.108
(for further references see the PDB file header)

Molecule 1 - THREE PRIME REPAIR EXONUCLEASE 1
	Chains	:	A, B, C, D
	EC Number	:	3.1.11.2
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PETM-10
	Expression System Strain	:	BL21
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	TREX1 EXONUCLEASE, UNP RESIDUES 9-245
	Gene	:	TREX1
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	3'-5' EXONUCLEASE TREX1

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 12)

No.	Name	Count	Type	Full Name
1	NA	4	Ligand/Ion	SODIUM ION
2	TMP	4	Ligand/Ion	THYMIDINE-5'-PHOSPHATE
3	ZN	4	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	NA	-1	Ligand/Ion	SODIUM ION
2	TMP	2	Ligand/Ion	THYMIDINE-5'-PHOSPHATE
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	NA	-1	Ligand/Ion	SODIUM ION
2	TMP	2	Ligand/Ion	THYMIDINE-5'-PHOSPHATE
3	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:18 , GLU A:20 , ASP A:200	BINDING SITE FOR RESIDUE ZN A 800
02	AC2	SOFTWARE	ASP A:18 , HOH A:1117 , HOH A:1119 , HOH A:1122	BINDING SITE FOR RESIDUE NA A 801
03	AC3	SOFTWARE	ASP B:18 , GLU B:20 , THR B:196 , ASP B:200	BINDING SITE FOR RESIDUE ZN B 800
04	AC4	SOFTWARE	ASP B:18 , HOH B:1097 , HOH B:1100 , HOH B:1101	BINDING SITE FOR RESIDUE NA B 801
05	AC5	SOFTWARE	ASP C:18 , GLU C:20 , ASP C:200	BINDING SITE FOR RESIDUE ZN C 800
06	AC6	SOFTWARE	ASP C:18 , HOH C:1100 , HOH C:1102 , HOH C:1103	BINDING SITE FOR RESIDUE NA C 801
07	AC7	SOFTWARE	ASP D:18 , GLU D:20 , ASP D:200	BINDING SITE FOR RESIDUE ZN D 800
08	AC8	SOFTWARE	ASP D:18 , HOH D:1132 , HOH D:1136 , HOH D:1138	BINDING SITE FOR RESIDUE NA D 801
09	AC9	SOFTWARE	ASP A:18 , LEU A:19 , GLU A:20 , ALA A:21 , LEU A:24 , ILE A:84 , THR A:85 , TYR A:129 , HIS A:195 , ASP A:200 , HOH A:1017 , HOH A:1118	BINDING SITE FOR RESIDUE TMP A 1000
10	BC1	SOFTWARE	ASP B:18 , LEU B:19 , GLU B:20 , ALA B:21 , GLY B:23 , LEU B:24 , ALA B:81 , ILE B:84 , THR B:85 , TYR B:129 , HIS B:195 , ASP B:200 , HOH B:1032 , HOH B:1099	BINDING SITE FOR RESIDUE TMP B 1000
11	BC2	SOFTWARE	ASP C:18 , LEU C:19 , GLU C:20 , ALA C:21 , ILE C:84 , THR C:85 , TYR C:129 , HIS C:195 , ASP C:200	BINDING SITE FOR RESIDUE TMP C 1000
12	BC3	SOFTWARE	ASP D:18 , LEU D:19 , GLU D:20 , ALA D:21 , ILE D:84 , THR D:85 , TYR D:129 , HIS D:195 , ASP D:200 , HOH D:1103 , HOH D:1134	BINDING SITE FOR RESIDUE TMP D 1000

(no "SS Bond" information available for 3B6P)

Asymmetric Unit

No.	Residues
1	His A:53	-	Pro A:54
2	Gln A:117	-	Pro A:118
3	His B:53	-	Pro B:54
4	Gln B:117	-	Pro B:118
5	His C:53	-	Pro C:54
6	Gln C:117	-	Pro C:118
7	His D:53	-	Pro D:54
8	Gln D:117	-	Pro D:118

(no "SAP(SNP)/Variant" information available for 3B6P)

(no "PROSITE Motif" information available for 3B6P)

(no "Exon" information available for 3B6P)

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:217
 aligned with TREX1_MOUSE | Q91XB0 from UniProtKB/Swiss-Prot  Length:314

    Alignment length:226
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228      
          TREX1_MOUSE     9 GHMQTLIFLDLEATGLPSSRPEVTELCLLAVHRRALENTSISQGHPPPVPRPPRVVDKLSLCIAPGKACSPGASEITGLSKAELEVQGRQRFDDNLAILLRAFLQRQPQPCCLVAHNGDRYDFPLLQTELARLSTPSPLDGTFCVDSIAALKALEQASSPSGNGSRKSYSLGSIYTRLYWQAPTDSHTAEGDVLTLLSICQWKPQALLQWVDEHARPFSTVKPMYG 234
               SCOP domains d3b6pa_ A: automated matches                                                                                                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeee..hhhhh..eeeeeeeeeehhhhhh..................eeeeee.......hhhhhhhhh.hhhhhhhh.....hhhhhhhhhhhhhh....eeeee.....hhhhhhhhhhhh..........eeeehhhhhhhhhh.---------...hhhhhhhhhhh.......hhhhhhhhhhhhhh.hhhhhhhhhhhhhee.hhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3b6p A   9 GHMQTLIFLDLEATGLPSSRPEVTELCLLAVHRRALENTSISQGHPPPVPRPPRVVDKLSLCIAPGKACSPGASEITGLSKAELEVQGRQRFDDNLAILLRAFLQRQPQPCCLVAHNGDRYDFPLLQTELARLSTPSPLDGTFCVDSIAALKALEQA---------KSYSLGSIYTRLYWQAPTDSHTAEGDVLTLLSICQWKPQALLQWVDEHARPFSTVKPMYG 234
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158      |  -      |178       188       198       208       218       228      
                                                                                                                                                                                      165       175

Chain B from PDB  Type:PROTEIN  Length:217
 aligned with TREX1_MOUSE | Q91XB0 from UniProtKB/Swiss-Prot  Length:314

    Alignment length:226
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228      
          TREX1_MOUSE     9 GHMQTLIFLDLEATGLPSSRPEVTELCLLAVHRRALENTSISQGHPPPVPRPPRVVDKLSLCIAPGKACSPGASEITGLSKAELEVQGRQRFDDNLAILLRAFLQRQPQPCCLVAHNGDRYDFPLLQTELARLSTPSPLDGTFCVDSIAALKALEQASSPSGNGSRKSYSLGSIYTRLYWQAPTDSHTAEGDVLTLLSICQWKPQALLQWVDEHARPFSTVKPMYG 234
               SCOP domains d3b6pb_ B: automated matches                                                                                                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeee..hhhhh..eeeeeeeeeehhhhhh..................eeeeee.......hhhhhhhhh.hhhhhhhh.....hhhhhhhhhhhhhh....eeeee.....hhhhhhhhhhhh..........eeeehhhhhhhhhh.---------...hhhhhhhhhhh.......hhhhhhhhhhhhhh.hhhhhhhhhhhhhee.hhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3b6p B   9 GHMQTLIFLDLEATGLPSSRPEVTELCLLAVHRRALENTSISQGHPPPVPRPPRVVDKLSLCIAPGKACSPGASEITGLSKAELEVQGRQRFDDNLAILLRAFLQRQPQPCCLVAHNGDRYDFPLLQTELARLSTPSPLDGTFCVDSIAALKALEQA---------KSYSLGSIYTRLYWQAPTDSHTAEGDVLTLLSICQWKPQALLQWVDEHARPFSTVKPMYG 234
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158      |  -      |178       188       198       208       218       228      
                                                                                                                                                                                      165       175

Chain C from PDB  Type:PROTEIN  Length:217
 aligned with TREX1_MOUSE | Q91XB0 from UniProtKB/Swiss-Prot  Length:314

    Alignment length:226
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228      
          TREX1_MOUSE     9 GHMQTLIFLDLEATGLPSSRPEVTELCLLAVHRRALENTSISQGHPPPVPRPPRVVDKLSLCIAPGKACSPGASEITGLSKAELEVQGRQRFDDNLAILLRAFLQRQPQPCCLVAHNGDRYDFPLLQTELARLSTPSPLDGTFCVDSIAALKALEQASSPSGNGSRKSYSLGSIYTRLYWQAPTDSHTAEGDVLTLLSICQWKPQALLQWVDEHARPFSTVKPMYG 234
               SCOP domains d3b6pc_ C: automated matches                                                                                                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeee..hhhhh..eeeeeeeeeehhhhhh..................eeeeee.......hhhhhhhhh.hhhhhhhh.....hhhhhhhhhhhhhh....eeeee.....hhhhhhhhhhhh..........eeeehhhhhhhhhh.---------...hhhhhhhhhhh.......hhhhhhhhhhhhhh.hhhhhhhhhhhhhee.hhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3b6p C   9 GHMQTLIFLDLEATGLPSSRPEVTELCLLAVHRRALENTSISQGHPPPVPRPPRVVDKLSLCIAPGKACSPGASEITGLSKAELEVQGRQRFDDNLAILLRAFLQRQPQPCCLVAHNGDRYDFPLLQTELARLSTPSPLDGTFCVDSIAALKALEQA---------KSYSLGSIYTRLYWQAPTDSHTAEGDVLTLLSICQWKPQALLQWVDEHARPFSTVKPMYG 234
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158      |  -      |178       188       198       208       218       228      
                                                                                                                                                                                      165       175

Chain D from PDB  Type:PROTEIN  Length:217
 aligned with TREX1_MOUSE | Q91XB0 from UniProtKB/Swiss-Prot  Length:314

    Alignment length:226
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228      
          TREX1_MOUSE     9 GHMQTLIFLDLEATGLPSSRPEVTELCLLAVHRRALENTSISQGHPPPVPRPPRVVDKLSLCIAPGKACSPGASEITGLSKAELEVQGRQRFDDNLAILLRAFLQRQPQPCCLVAHNGDRYDFPLLQTELARLSTPSPLDGTFCVDSIAALKALEQASSPSGNGSRKSYSLGSIYTRLYWQAPTDSHTAEGDVLTLLSICQWKPQALLQWVDEHARPFSTVKPMYG 234
               SCOP domains d3b6pd_ D: automated matches                                                                                                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeee..hhhhh..eeeeeeeeeehhhhhh..................eeeeee.......hhhhhhhhh.hhhhhhhh.....hhhhhhhhhhhhhh....eeeee.....hhhhhhhhhhhh..........eeeehhhhhhhhhh.---------...hhhhhhhhhhh.......hhhhhhhhhhhhhh.hhhhhhhhhhhhhee.hhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3b6p D   9 GHMQTLIFLDLEATGLPSSRPEVTELCLLAVHRRALENTSISQGHPPPVPRPPRVVDKLSLCIAPGKACSPGASEITGLSKAELEVQGRQRFDDNLAILLRAFLQRQPQPCCLVAHNGDRYDFPLLQTELARLSTPSPLDGTFCVDSIAALKALEQA---------KSYSLGSIYTRLYWQAPTDSHTAEGDVLTLLSICQWKPQALLQWVDEHARPFSTVKPMYG 234
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158      |  -      |178       188       198       208       218       228      
                                                                                                                                                                                      165       175

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 Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: Ribonuclease H-like motif (1424)

Superfamily: Ribonuclease H-like (775)

Family: automated matches (127)

Protein domain: automated matches (127)

Mouse (Mus musculus) [TaxId: 10090] (6)

1a	d3b6pa_	A:
1b	d3b6pb_	B:
1c	d3b6pc_	C:
1d	d3b6pd_	D:

(no "CATH Domain" information available for 3B6P)

(no "Pfam Domain" information available for 3B6P)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (TREX1_MOUSE | Q91XB0)

molecular function
	GO:0008408	3'-5' exonuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' end.
	GO:0008296	3'-5'-exodeoxyribonuclease activity	Catalysis of the sequential cleavage of mononucleotides from a free 3' terminus of a DNA molecule.
	GO:0032405	MutLalpha complex binding	Interacting selectively and non-covalently with the mismatch repair complex MutLalpha.
	GO:0032407	MutSalpha complex binding	Interacting selectively and non-covalently with the mismatch repair complex MutSalpha.
	GO:0032558	adenyl deoxyribonucleotide binding	Interacting selectively and non-covalently with an adenyl deoxyribonucleotide, any compound consisting of adenosine esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the deoxyribose moiety.
	GO:0003690	double-stranded DNA binding	Interacting selectively and non-covalently with double-stranded DNA.
	GO:0008853	exodeoxyribonuclease III activity	Catalysis of the degradation of double-stranded DNA. It acts progressively in a 3' to 5' direction, releasing 5'-phosphomononucleotides.
	GO:0004527	exonuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0004518	nuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids.
	GO:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
	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:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
	GO:0003697	single-stranded DNA binding	Interacting selectively and non-covalently with single-stranded DNA.
biological process
	GO:0006259	DNA metabolic process	Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides.
	GO:0035458	cellular response to interferon-beta	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an interferon-beta stimulus. Interferon-beta is a type I interferon.
	GO:0090305	nucleic acid phosphodiester bond hydrolysis	The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
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:0005783	endoplasmic reticulum	The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
	GO:0005789	endoplasmic reticulum membrane	The lipid bilayer surrounding the endoplasmic reticulum.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	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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	Cis Peptide Bonds
		Gln A:117 - Pro A:118	[ RasMol ]
		Gln B:117 - Pro B:118	[ RasMol ]
		Gln C:117 - Pro C:118	[ RasMol ]
		Gln D:117 - Pro D:118	[ RasMol ]
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	3b6p
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	TREX1_MOUSE \| Q91XB0
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	3.1.11.2
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	TREX1_MOUSE \| Q91XB0
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	TREX1_MOUSE \| Q91XB0	:	2ioc 2o4g 2o4i 2oa8 3b6o 3mxi 3mxj 3mxm 3u3y 3u6f 4ynq

1y97	TREX2, THE TREX1 HOMOLOGUE
2ioc	THE CRYSTAL STRUCTURE OF TREX1 EXPLAINS THE 3' NUCLEOTIDE SPECIFICITY AND REVEALS A POLYPROLINE II HELIX FOR PROTEIN PARTENRING
2o4g	STRUCTURE OF TREX1 IN COMPLEX WITH A NUCLEOTIDE
2o4i	STRUCTURE OF TREX1 IN COMPLEX WITH DNA
2oa8	CRYSTAL STRUCTURE OF MTREX1 WITH SSDNA
3b6o	STRUCTURE OF TREX1 IN COMPLEX WITH A NUCLEOTIDE AND AN INHIBITOR ION (LITHIUM)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 12)

Sites (12, 12)

SS Bonds (0, 0)

Cis Peptide Bonds (8, 8)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 4)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (24, 24)

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