3FCL - JenaLib

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Title :   COMPLEX OF UNG2 AND A FRAGMENT-BASED DESIGNED INHIBITOR

Authors :   M. A. Bianchet, S. Chung, J. B. Parker, L. M. Amzel, J. T. Stivers

Date :   21 Nov 08 (Deposition) - 28 Apr 09 (Release) - 02 Jun 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

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

Keywords :   Dna Repair, Uracil, Uracil Dna Glycosylase, Alternative Splicing, Disease Mutation, Dna Damage, Glycosidase, Host- Virus Interaction, Hydrolase, Mitochondrion, Nucleus, Phosphoprotein, Transit Peptide (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Chung, J. B. Parker, M. Bianchet, L. M. Amzel, J. T. Stivers
Impact Of Linker Strain And Flexibility In The Design Of A Fragment-Based Inhibitor
Nat. Chem. Biol. V. 5 407 2009
PubMed-ID: 19396178 | Reference-DOI: 10.1038/NCHEMBIO.163
(for further references see the PDB file header)

Molecule 1 - URACIL-DNA GLYCOSYLASE
	Chains	:	A, B
	EC Number	:	3.2.2.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	UNG, DGU, UNG1, UNG15
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	UDG

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 10)

No.	Name	Count	Type	Full Name
1	3FL	2	Ligand/Ion	3-{[(4-{[(2,6-DIOXO-1,2,3,6-TETRAHYDROPYRIMIDIN-4-YL)METHYL]AMINO}BUTYL)AMINO]METHYL}BENZOIC ACID
2	SCN	8	Ligand/Ion	THIOCYANATE ION

Biological Unit 1 (2, 5)

No.	Name	Count	Type	Full Name
1	3FL	1	Ligand/Ion	3-{[(4-{[(2,6-DIOXO-1,2,3,6-TETRAHYDROPYRIMIDIN-4-YL)METHYL]AMINO}BUTYL)AMINO]METHYL}BENZOIC ACID
2	SCN	4	Ligand/Ion	THIOCYANATE ION

Biological Unit 2 (2, 5)

No.	Name	Count	Type	Full Name
1	3FL	1	Ligand/Ion	3-{[(4-{[(2,6-DIOXO-1,2,3,6-TETRAHYDROPYRIMIDIN-4-YL)METHYL]AMINO}BUTYL)AMINO]METHYL}BENZOIC ACID
2	SCN	4	Ligand/Ion	THIOCYANATE ION

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HOH A:20 , GLY A:143 , GLN A:144 , ASP A:145 , TYR A:147 , CYS A:157 , PHE A:158 , ASN A:204 , SER A:270 , SER A:273 , HOH A:339 , HOH A:400 , GLU B:83 , PHE B:84 , PHE B:85 , LYS B:90 , HOH B:444	BINDING SITE FOR RESIDUE 3FL A 1
02	AC2	SOFTWARE	MET A:106 , VAL A:109 , ARG A:113 , VAL A:125 , ARG B:276	BINDING SITE FOR RESIDUE SCN A 2
03	AC3	SOFTWARE	TYR A:147 , PRO A:167 , SER A:169 , HOH A:397 , HOH A:427 , SCN B:8	BINDING SITE FOR RESIDUE SCN A 5
04	AC4	SOFTWARE	PRO A:168 , ASN A:172 , PRO A:271 , HOH A:336 , GLY B:98 , ILE B:103 , HOH B:449	BINDING SITE FOR RESIDUE SCN A 6
05	AC5	SOFTWARE	SER A:270 , HOH A:399 , SCN B:8 , LYS B:90 , PHE B:97	BINDING SITE FOR RESIDUE SCN A 7
06	AC6	SOFTWARE	GLU A:83 , PHE A:84 , HOH A:367 , SCN B:4 , HOH B:47 , GLY B:143 , GLN B:144 , ASP B:145 , TYR B:147 , CYS B:157 , PHE B:158 , SER B:169 , ASN B:204 , HIS B:268 , SER B:270 , SER B:273 , HOH B:327 , HOH B:346 , HOH B:386 , HOH B:499 , HOH B:500	BINDING SITE FOR RESIDUE 3FL B 2
07	AC7	SOFTWARE	MET B:106 , VAL B:109 , ARG B:113 , VAL B:125	BINDING SITE FOR RESIDUE SCN B 1
08	AC8	SOFTWARE	PHE B:184 , ILE B:299 , TRP B:301 , LYS B:302	BINDING SITE FOR RESIDUE SCN B 3
09	AC9	SOFTWARE	LYS A:90 , PHE A:97 , 3FL B:2 , SER B:270 , PRO B:271	BINDING SITE FOR RESIDUE SCN B 4
10	BC1	SOFTWARE	SCN A:5 , SCN A:7 , PRO A:168 , PRO A:271 , SER B:94	BINDING SITE FOR RESIDUE SCN B 8

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

Asymmetric Unit

No.	Residues
1	Tyr A:119	-	Pro A:120
2	Arg A:162	-	Pro A:163
3	Tyr B:119	-	Pro B:120
4	Arg B:162	-	Pro B:163

Asymmetric Unit (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_017094	F	251	S	UNG_HUMAN	Disease (HIGM5)	104894380	A/B	F	242	S

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

Biological Unit 1 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_017094	F	251	S	UNG_HUMAN	Disease (HIGM5)	104894380	A	F	242	S

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

Biological Unit 2 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_017094	F	251	S	UNG_HUMAN	Disease (HIGM5)	104894380	B	F	242	S

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	U_DNA_GLYCOSYLASE	PS00130	Uracil-DNA glycosylase signature.	UNG_HUMAN	147-156	2	A:138-147 B:138-147

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	U_DNA_GLYCOSYLASE	PS00130	Uracil-DNA glycosylase signature.	UNG_HUMAN	147-156	1	A:138-147 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	U_DNA_GLYCOSYLASE	PS00130	Uracil-DNA glycosylase signature.	UNG_HUMAN	147-156	1	- B:138-147

Asymmetric Unit (6, 12)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000242576	1	ENSE00001130047	chr12:109535415-109535616	202	UNG_HUMAN	1-44	44	0	-	-
1.2c	ENST00000242576	2c	ENSE00001130067	chr12:109536237-109536443	207	UNG_HUMAN	45-113	69	2	A:83-104 B:83-104	22 22
1.3	ENST00000242576	3	ENSE00000754701	chr12:109536994-109537089	96	UNG_HUMAN	114-145	32	2	A:105-136 B:105-136	32 32
1.4	ENST00000242576	4	ENSE00000754703	chr12:109539707-109539804	98	UNG_HUMAN	146-178	33	2	A:137-169 B:137-169	33 33
1.5	ENST00000242576	5	ENSE00000754705	chr12:109540644-109540732	89	UNG_HUMAN	178-208	31	2	A:169-199 B:169-199	31 31
1.6	ENST00000242576	6	ENSE00000834681	chr12:109541238-109541416	179	UNG_HUMAN	208-267	60	2	A:199-258 B:199-258	60 60
1.7	ENST00000242576	7	ENSE00001130061	chr12:109547634-109548798	1165	UNG_HUMAN	268-313	46	2	A:259-304 B:259-304	46 46

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:222
 aligned with UNG_HUMAN | P13051 from UniProtKB/Swiss-Prot  Length:313

    Alignment length:222
                                   101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311  
            UNG_HUMAN    92 VGFGESWKKHLSGEFGKPYFIKLMGFVAEERKHYTVYPPPHQVFTWTQMCDIKDVKVVILGQDPYHGPNQAHGLCFSVQRPVPPPPSLENIYKELSTDIEDFVHPGHGDLSGWAKQGVLLLNAVLTVRAHQANSHKERGWEQFTDAVVSWLNQNSNGLVFLLWGSYAQKKGSAIDRKRHHVLQTAHPSPLSVYRGFFGCRHFSKTNELLQKSGKKPIDWKEL 313
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 3fclA00 A:83-304 Uracil-DNA Glycosylase, subunit E                                                                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.ee.hhhhhhhhhh..hhhhh.eeeee.......................hhhhhhhhhhhhhhh..........hhhhhhh.eeeee....ee..........hhhhhhhhhhhhhhhhh...eeeeehhhhhhhh........eeeee......hhhhh....hhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------S-------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------U_DNA_GLYC------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2c [INCOMPLETE]Exon 1.3  PDB: A:105-136        Exon 1.4  PDB: A:137-169         -----------------------------Exon 1.6  PDB: A:199-258 UniProt: 208-267                   Exon 1.7  PDB: A:259-304 UniProt: 268-313      Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------------------------Exon 1.5  PDB: A:169-199       --------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 3fcl A  83 EFFGESWKKHLSGEFGKPYFIKLMGFVAEERKHYTVYPPPHQVFTWTQMCDIKDVKVVILGQDPYHGPNQAHGLCFSVQRPVPPPPSLENIYKELSTDIEDFVHPGHGDLSGWAKQGVLLLNAVLTVRAHQANSHKERGWEQFTDAVVSWLNQNSNGLVFLLWGSYAQKKGSAIDRKRHHVLQTAHPSPLSVYRGFFGCRHFSKTNELLQKSGKKPIDWKEL 304
                                    92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302

Chain B from PDB  Type:PROTEIN  Length:222
 aligned with UNG_HUMAN | P13051 from UniProtKB/Swiss-Prot  Length:313

    Alignment length:222
                                   101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311  
            UNG_HUMAN    92 VGFGESWKKHLSGEFGKPYFIKLMGFVAEERKHYTVYPPPHQVFTWTQMCDIKDVKVVILGQDPYHGPNQAHGLCFSVQRPVPPPPSLENIYKELSTDIEDFVHPGHGDLSGWAKQGVLLLNAVLTVRAHQANSHKERGWEQFTDAVVSWLNQNSNGLVFLLWGSYAQKKGSAIDRKRHHVLQTAHPSPLSVYRGFFGCRHFSKTNELLQKSGKKPIDWKEL 313
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 3fclB00 B:83-304 Uracil-DNA Glycosylase, subunit E                                                                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.ee.hhhhhhhhhh..hhhhh.eeeee.......................hhhhhhhhhhhhhhh..........hhhhhh..eeeee....ee..........hhhhhhhhhhhhhhhhh...eeeeehhhhhh..........eeeee......hhhhh....hhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------S-------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------U_DNA_GLYC------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2c [INCOMPLETE]Exon 1.3  PDB: B:105-136        Exon 1.4  PDB: B:137-169         -----------------------------Exon 1.6  PDB: B:199-258 UniProt: 208-267                   Exon 1.7  PDB: B:259-304 UniProt: 268-313      Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------------------------Exon 1.5  PDB: B:169-199       --------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 3fcl B  83 EFFGESWKKHLSGEFGKPYFIKLMGFVAEERKHYTVYPPPHQVFTWTQMCDIKDVKVVILGQDPYHGPNQAHGLCFSVQRPVPPPPSLENIYKELSTDIEDFVHPGHGDLSGWAKQGVLLLNAVLTVRAHQANSHKERGWEQFTDAVVSWLNQNSNGLVFLLWGSYAQKKGSAIDRKRHHVLQTAHPSPLSVYRGFFGCRHFSKTNELLQKSGKKPIDWKEL 304
                                    92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302

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 '\|'

(no "SCOP Domain" information available for 3FCL)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

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

Topology: Uracil-DNA Glycosylase, subunit E (52)

Homologous Superfamily: Uracil-DNA Glycosylase, subunit E (52)

Human (Homo sapiens) (10)

1a	3fclA00	A:83-304
1b	3fclB00	B:83-304

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (UNG_HUMAN | P13051)

molecular function
	GO:0003684	damaged DNA binding	Interacting selectively and non-covalently with damaged DNA.
	GO:0019899	enzyme binding	Interacting selectively and non-covalently with any enzyme.
	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:0016798	hydrolase activity, acting on glycosyl bonds	Catalysis of the hydrolysis of any glycosyl bond.
	GO:0016799	hydrolase activity, hydrolyzing N-glycosyl compounds	Catalysis of the hydrolysis of any N-glycosyl bond.
	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:0004844	uracil DNA N-glycosylase activity	Catalysis of the cleavage of the N-C1' glycosidic bond between the damaged DNA base and the deoxyribose sugar, releasing a free base and leaving an apyrimidinic (AP) site. Enzymes with this activity recognize and remove uracil bases in DNA that result from the deamination of cytosine or the misincorporation of dUTP opposite an adenine.
biological process
	GO:0006281	DNA repair	The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
	GO:0006284	base-excision repair	In base excision repair, an altered base is removed by a DNA glycosylase enzyme, followed by excision of the resulting sugar phosphate. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase.
	GO:0097510	base-excision repair, AP site formation via deaminated base removal	A base-excision repair, AP site formation process occurring via excision of a deaminated base.
	GO:0006974	cellular response to DNA damage stimulus	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 a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
	GO:0045008	depyrimidination	The disruption of the bond between the sugar in the backbone and the C or T base, causing the base to be removed and leaving a depyrimidinated sugar.
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	GO:0043066	negative regulation of apoptotic process	Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
	GO:0045830	positive regulation of isotype switching	Any process that activates or increases the frequency, rate or extent of isotype switching.
	GO:0016446	somatic hypermutation of immunoglobulin genes	Mutations occurring somatically that result in amino acid changes in the rearranged V regions of immunoglobulins.
	GO:0016447	somatic recombination of immunoglobulin gene segments	The process in which immunoglobulin genes are formed through recombination of the germline genetic elements, as known as immunoglobulin gene segments, within a single locus.
	GO:0016032	viral process	A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	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
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		Tyr A:119 - Pro A:120	[ RasMol ]
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Description

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