1NOP | PD0391 - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HUMAN TYROSYL-DNA PHOSPHODIESTERASE (TDP1) IN COMPLEX WITH VANADATE, DNA AND A HUMAN TOPOISOMERASE I-DERIVED PEPTIDE

Authors :   D. R. Davies, H. Interthal, J. J. Champoux, W. G. J. Hol

Date :   16 Jan 03 (Deposition) - 11 Mar 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Protein-Dna Complex, Vanadate Complex, Transition State Mimic, Hydrolase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. R. Davies, H. Interthal, J. J. Champoux, W. G. J. Hol
Crystal Structure Of A Transition State Mimic For Tdp1 Assembled From Vanadate, Dna, And A Topoisomerase I-Derived Peptide
Chem. Biol. V. 10 139 2003
PubMed-ID: 12618186 | Reference-DOI: 10.1016/S1074-5521(03)00021-8
(for further references see the PDB file header)

*Molecule 1 - 5'-D(APGPAPGPTPT)-3'*
	Chains	:	D, F
	Engineered	:	YES
	Other Details	:	THIS SEQUENCE IS DERIVED FROM A SEQUENCE KNOWN TO BE A TARGET FOR TOPOISOMERASE I
	Synthetic	:	YES

Molecule 2 - TYROSYL-DNA PHOSPHODIESTERASE 1
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PET15B
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 149-608
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	TDP1

Molecule 3 - TOPOISOMERASE I-DERIVED PEPTIDE
	Chains	:	C
	Engineered	:	YES
	Fragment	:	RESIDUES 720-727
	Other Details	:	THIS SEQUENCE OCCURS NATURALLY IN HUMAN TOPOISOMERASE I. THIS SEQUENCE INCLUDES THE CATALYTIC TYROSINE RESIDUE THAT BECOMES TRANSIENTLY COVALENTLY ATTATCHED TO THE 3' END OF DNA
	Synthetic	:	YES

		1	2	3	4	5
Asymmetric Unit	:	A	B	C	D	F
Biological Unit 1 (1x)	:	A		C	D
Biological Unit 2 (1x)	:		B			F

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	VO4	2	Ligand/Ion	VANADATE ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	VO4	1	Ligand/Ion	VANADATE ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	VO4	1	Ligand/Ion	VANADATE ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:263 , LYS A:265 , ASN A:283 , HIS A:493 , LYS A:495 , ASN A:516 , HOH A:728 , TYR C:723 , DT D:806	BINDING SITE FOR RESIDUE VO4 A 699
2	AC2	SOFTWARE	TYR B:204 , HIS B:263 , LYS B:265 , ASN B:283 , HIS B:493 , LYS B:495 , ASN B:516 , DT F:806	BINDING SITE FOR RESIDUE VO4 B 699

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

Asymmetric Unit

No.	Residues
1	Leu A:576	-	Pro A:577
2	Leu B:576	-	Pro B:577

Asymmetric Unit (4, 8)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_025820	D	187	G	TYDP1_HUMAN	Polymorphism	35271143	A/B	D	187	G
2	UniProt	VAR_025821	R	304	Q	TYDP1_HUMAN	Polymorphism	34452707	A/B	R	304	Q
3	UniProt	VAR_017144	H	493	R	TYDP1_HUMAN	Disease (SCAN1)	119467003	A/B	H	493	R
4	UniProt	VAR_025822	T	569	A	TYDP1_HUMAN	Polymorphism	35973343	A/B	T	569	A

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

Biological Unit 1 (4, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_025820	D	187	G	TYDP1_HUMAN	Polymorphism	35271143	A	D	187	G
2	UniProt	VAR_025821	R	304	Q	TYDP1_HUMAN	Polymorphism	34452707	A	R	304	Q
3	UniProt	VAR_017144	H	493	R	TYDP1_HUMAN	Disease (SCAN1)	119467003	A	H	493	R
4	UniProt	VAR_025822	T	569	A	TYDP1_HUMAN	Polymorphism	35973343	A	T	569	A

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

Biological Unit 2 (4, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_025820	D	187	G	TYDP1_HUMAN	Polymorphism	35271143	B	D	187	G
2	UniProt	VAR_025821	R	304	Q	TYDP1_HUMAN	Polymorphism	34452707	B	R	304	Q
3	UniProt	VAR_017144	H	493	R	TYDP1_HUMAN	Disease (SCAN1)	119467003	B	H	493	R
4	UniProt	VAR_025822	T	569	A	TYDP1_HUMAN	Polymorphism	35973343	B	T	569	A

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

(no "PROSITE Motif" information available for 1NOP)

Asymmetric Unit (15, 30)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000393454	1	ENSE00001413418	chr14:90422246-90422314	69	TYDP1_HUMAN	-	0	0	-	-
1.3	ENST00000393454	3	ENSE00002191997	chr14:90429452-90430017	566	TYDP1_HUMAN	1-187	187	2	A:162-187 B:159-187	26 29
1.4	ENST00000393454	4	ENSE00001794647	chr14:90432491-90432534	44	TYDP1_HUMAN	187-201	15	2	A:187-201 B:187-201	15 15
1.5	ENST00000393454	5	ENSE00001653050	chr14:90433711-90433766	56	TYDP1_HUMAN	202-220	19	2	A:202-220 B:202-220	19 19
1.6	ENST00000393454	6	ENSE00001773975	chr14:90437519-90437615	97	TYDP1_HUMAN	220-252	33	2	A:220-252 B:220-252	33 33
1.7	ENST00000393454	7	ENSE00000912013	chr14:90442125-90442159	35	TYDP1_HUMAN	253-264	12	2	A:253-264 B:253-264	12 12
1.8	ENST00000393454	8	ENSE00001146713	chr14:90446884-90446976	93	TYDP1_HUMAN	264-295	32	2	A:264-295 B:264-295	32 32
1.9	ENST00000393454	9	ENSE00001146704	chr14:90450860-90451027	168	TYDP1_HUMAN	295-351	57	2	A:295-351 B:295-351	57 57
1.10	ENST00000393454	10	ENSE00001146697	chr14:90451476-90451554	79	TYDP1_HUMAN	351-377	27	2	A:351-377 B:351-377	27 27
1.11	ENST00000393454	11	ENSE00001146688	chr14:90455249-90455434	186	TYDP1_HUMAN	378-439	62	2	A:378-439 (gaps) B:378-439 (gaps)	62 62
1.12	ENST00000393454	12	ENSE00001146680	chr14:90456061-90456109	49	TYDP1_HUMAN	440-456	17	2	A:440-456 B:440-456	17 17
1.13	ENST00000393454	13	ENSE00001146670	chr14:90458261-90458327	67	TYDP1_HUMAN	456-478	23	2	A:456-478 B:456-478	23 23
1.14	ENST00000393454	14	ENSE00001146662	chr14:90459720-90459827	108	TYDP1_HUMAN	478-514	37	2	A:478-514 B:478-514	37 37
1.15	ENST00000393454	15	ENSE00001146656	chr14:90485660-90485762	103	TYDP1_HUMAN	514-548	35	2	A:514-548 B:514-548	35 35
1.17	ENST00000393454	17	ENSE00001760418	chr14:90499450-90499558	109	TYDP1_HUMAN	549-585	37	2	A:549-585 (gaps) B:549-585 (gaps)	37 37
1.18	ENST00000393454	18	ENSE00001596585	chr14:90509414-90511106	1693	TYDP1_HUMAN	585-608	24	2	A:585-608 B:585-607	24 23

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:425
 aligned with TYDP1_HUMAN | Q9NUW8 from UniProtKB/Swiss-Prot  Length:608

    Alignment length:447
                                   171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       
          TYDP1_HUMAN   162 NPFQFYLTRVSGVKPKYNSGALHIKDILSPLFGTLVSSAQFNYCFDVDWLVKQYPPEFRKKPILLVHGDKREAKAHLHAQAKPYENISLCQAKLDIAFGTHHTKMMLLLYEEGLRVVIHTSNLIHADWHQKTQGIWLSPLYPRIADGTHKSGESPTHFKADLISYLMAYNAPSLKEWIDVIHKHDLSETNVYLIGSTPGRFQGSQKDNWGHFRLKKLLKDHASSMPNAESWPVVGQFSSVGSLGADESKWLCSEFKESMLTLGKESKTPGKSSVPLYLIYPSVENVRTSLEGYPAGGSLPYSIQTAEKQNWLHSYFHKWSAETSGRSNAMPHIKTYMRPSPDFSKIAWFLVTSANLSKAAWGALEKNGTQLMIRSYELGVLFLPSAFGLDSFKVKQKFFAGSQEPMATFPVPYDLPPELYGSKDRPWIWNIPYVKAPDTHGNMWVPS 608
               SCOP domains d1nopa1 A:162-350 Tyrosyl-DNA phosphodiesterase TDP1                                                                                                                                         d1nopa2 A:351-608 Tyrosyl-DNA phosph    odiesterase TDP1                                                                                                                                                                                                           SCOP domains
               CATH domains 1nopA01 A:162-351 Endonuclease Chain A                                                                                                                                                        1nopA02 A:352-608 Phospholipase D/n    uclease; domain 2                                                                                                                                                                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee......hhhhh....hhhhhhhhhhh.eeeeeee....hhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhh....eeeee.............eeeeee...eeeeee....hhhhhh....eeee...................hhhhhhhhhhhh..hhhhhhhhhhhhhh.......eeeee..eeehhhhhhhhhhhhhhhhhhhhh...----...eeee................hhhhhhhhh..----------..eeee..hhhhhhh...hhhhhhhh..hhhhhhhhhhhhh.ee...hhhhh.........eeeee.....eeeeeeee....hhhhhheee....eeee...eeeeeehhhhhh...eee....--------.ee...................................... Sec.struct. author
                 SAPs(SNPs) -------------------------G--------------------------------------------------------------------------------------------------------------------Q--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------R---------------------------------------------------------------------------A--------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3  PDB: A:162-187  --------------Exon 1.5           --------------------------------Exon 1.7    --------------------------------------------------------------------------------------Exon 1.10  PDB: A:351-377  Exon 1.11  PDB: A:378-439 (gaps) UniProt: 378-439             Exon 1.12        ---------------------Exon 1.14  PDB: A:478-514            ----------------------------------Exon 1.17  PDB: A:549-585 (gaps)     ----------------------- Transcript 1 (1)
           Transcript 1 (2) -------------------------Exon 1.4       ------------------Exon 1.6  PDB: A:220-252         -----------Exon 1.8  PDB: A:264-295        ----------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.13              -----------------------------------Exon 1.15  PDB: A:514-548          ------------------------------------Exon 1.18  PDB: A:585-60 Transcript 1 (2)
           Transcript 1 (3) -------------------------------------------------------------------------------------------------------------------------------------Exon 1.9  PDB: A:295-351 UniProt: 295-351                ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (3)
                 1nop A 162 NPFQFYLTRVSGVKPKYNSGALHIKDILSPLFGTLVSSAQFNYCFDVDWLVKQYPPEFRKKPILLVHGDKREAKAHLHAQAKPYENISLCQAKLDIAFGTHHTKMMLLLYEEGLRVVIHTSNLIHADWHQKTQGIWLSPLYPRIADGTHKSGESPTHFKANLISYLTAYNAPSLKEWIDVIHKHDLSETNVYLIGSTPGRFQGSQKDNWGHFRLKKLLKDHASSM----SWPVVGQFSSVGSLGADESKWLCSEFKESMLTLG----------VPLYLIYPSVENVRTSLEGYPAGGSLPYSIQTAEKQNWLHSYFHKWSAETSGRSNAMPHIKTYMRPSPDFSKIAWFLVTSANLSKAAWGALEKNGTQLMIRSYELGVLFLPSALGLDSFKVKQKF--------ATFPVPYDLPPELYGSKDRPWIWNIPYVKAPDTHGNMWVPS 608
                                   171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381    |  391       401       411       421  |      -   |   441       451       461       471       481       491       501       511       521       531       541       551       | -      |571       581       591       601       
                                                                                                                                                                                                                                                          386  391                              424        435                                                                                                                         559      568

Chain B from PDB  Type:PROTEIN  Length:433
 aligned with TYDP1_HUMAN | Q9NUW8 from UniProtKB/Swiss-Prot  Length:608

    Alignment length:449
                                   168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598         
          TYDP1_HUMAN   159 DKGNPFQFYLTRVSGVKPKYNSGALHIKDILSPLFGTLVSSAQFNYCFDVDWLVKQYPPEFRKKPILLVHGDKREAKAHLHAQAKPYENISLCQAKLDIAFGTHHTKMMLLLYEEGLRVVIHTSNLIHADWHQKTQGIWLSPLYPRIADGTHKSGESPTHFKADLISYLMAYNAPSLKEWIDVIHKHDLSETNVYLIGSTPGRFQGSQKDNWGHFRLKKLLKDHASSMPNAESWPVVGQFSSVGSLGADESKWLCSEFKESMLTLGKESKTPGKSSVPLYLIYPSVENVRTSLEGYPAGGSLPYSIQTAEKQNWLHSYFHKWSAETSGRSNAMPHIKTYMRPSPDFSKIAWFLVTSANLSKAAWGALEKNGTQLMIRSYELGVLFLPSAFGLDSFKVKQKFFAGSQEPMATFPVPYDLPPELYGSKDRPWIWNIPYVKAPDTHGNMWVP 607
               SCOP domains d1nopb1 B:159-350 Tyrosyl-DNA phosphodiesterase TDP1                                                                                                                                            d1nopb2 B:351-607 Tyrosyl-DNA phosphodiesterase TDP1                                                                                                                                                                                                              SCOP domains
               CATH domains 1nopB01 B:159-351 Endonuclease Chain A                                                                                                                                                           1nopB02 B:352-607 Phospholipase D/nuclease; domain 2                                                                                                                                                                                                             CATH domains
           Pfam domains (1) ----Tyr-DNA_phospho-1nopB01 B:163-582                                                                                                                                                                                                                                                                                                                                                                                                   ------------------------- Pfam domains (1)
           Pfam domains (2) ----Tyr-DNA_phospho-1nopB02 B:163-582                                                                                                                                                                                                                                                                                                                                                                                                   ------------------------- Pfam domains (2)
         Sec.struct. author .......eee......hhhhh....hhhhhhhhhhh.eeeeeee....hhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhh....eeeee.............eeeeee...eeeeee.....hhhhh....eeee...................hhhhhhhhhhhh..hhhhhhhhhhhhh........eeeee..eeehhhhhhhhhhhhhhhhhhhhh....hhhhh.eeee.................hhhhhhh...---------...eeee..hhhhhhh...hhhhhhhh..hhhhhhhhhhhhh.ee...hhhhh........eeeeee.....eeeeeeee....hhhhhheee....eeee...eeeeeehhhhhh...eee....-------..ee..................................... Sec.struct. author
                 SAPs(SNPs) ----------------------------G--------------------------------------------------------------------------------------------------------------------Q--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------R---------------------------------------------------------------------------A-------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3  PDB: B:159-187     --------------Exon 1.5           --------------------------------Exon 1.7    --------------------------------------------------------------------------------------Exon 1.10  PDB: B:351-377  Exon 1.11  PDB: B:378-439 (gaps) UniProt: 378-439             Exon 1.12        ---------------------Exon 1.14  PDB: B:478-514            ----------------------------------Exon 1.17  PDB: B:549-585 (gaps)     ---------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------Exon 1.4       ------------------Exon 1.6  PDB: B:220-252         -----------Exon 1.8  PDB: B:264-295        ----------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.13              -----------------------------------Exon 1.15  PDB: B:514-548          ------------------------------------Exon 1.18 [INCOMPLETE]  Transcript 1 (2)
           Transcript 1 (3) ----------------------------------------------------------------------------------------------------------------------------------------Exon 1.9  PDB: B:295-351 UniProt: 295-351                ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (3)
                 1nop B 159 DKGNPFQFYLTRVSGVKPKYNSGALHIKDILSPLFGTLVSSAQFNYCFDVDWLVKQYPPEFRKKPILLVHGDKREAKAHLHAQAKPYENISLCQAKLDIAFGTHHTKMMLLLYEEGLRVVIHTSNLIHADWHQKTQGIWLSPLYPRIADGTHKSGESPTHFKANLISYLTAYNAPSLKEWIDVIHKHDLSETNVYLIGSTPGRFQGSQKDNWGHFRLKKLLKDHASSMPNAESWPVVGQFSSVGSLGADESKWLCSEFKESMLTLG---------SVPLYLIYPSVENVRTSLEGYPAGGSLPYSIQTAEKQNWLHSYFHKWSAETSGRSNAMPHIKTYMRPSPDFSKIAWFLVTSANLSKAAWGALEKNGTQLMIRSYELGVLFLPSALGLDSFKVKQKF-------MATFPVPYDLPPELYGSKDRPWIWNIPYVKAPDTHGNMWVP 607
                                   168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418     |   -     | 438       448       458       468       478       488       498       508       518       528       538       548       558|      568       578       588       598         
                                                                                                                                                                                                                                                                                                   424       434                                                                                                                          559     567

Chain C from PDB  Type:PROTEIN  Length:5
                                     
               SCOP domains ----- SCOP domains
               CATH domains ----- CATH domains
               Pfam domains ----- Pfam domains
         Sec.struct. author ..... Sec.struct. author
                 SAPs(SNPs) ----- SAPs(SNPs)
                    PROSITE ----- PROSITE
                 Transcript ----- Transcript
                 1nop C 720 KLNYL 724

Chain D from PDB  Type:DNA  Length:3
                                   
                 1nop D 804 GTT 806

Chain F from PDB  Type:DNA  Length:1
                                 
                 1nop F 804 T 806

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) (23004)

Fold: Phospholipase D/nuclease (33)

Superfamily: Phospholipase D/nuclease (33)

Family: Tyrosyl-DNA phosphodiesterase TDP1 (17)

Protein domain: Tyrosyl-DNA phosphodiesterase TDP1 (13)

Human (Homo sapiens) [TaxId: 9606] (12)

1a	d1nopa1	A:162-350
1b	d1nopa2	A:351-608
1c	d1nopb1	B:159-350
1d	d1nopb2	B:351-607

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Endonuclease; Chain A (28)

Homologous Superfamily: Endonuclease Chain A (28)

[unclassified] (8)

1a	1nopB01	B:159-351
1b	1nopA01	A:162-351

Homologous Superfamily: Phospholipase D/nuclease; domain 2 (13)

[unclassified] (8)

2a	1nopA02	A:352-608
2b	1nopB02	B:352-607

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: PLD (22)

Family: Tyr-DNA_phospho (11)

Homo sapiens (Human) (10)

1a	Tyr-DNA_phospho-1nopB01	B:163-582
1b	Tyr-DNA_phospho-1nopB02	B:163-582

Asymmetric Unit(hide GO term definitions)

Chain A,B (TYDP1_HUMAN | Q9NUW8)

molecular function
	GO:0017005	3'-tyrosyl-DNA phosphodiesterase activity	Catalysis of the hydrolysis of 3'-phosphotyrosyl groups formed as covalent intermediates (in DNA backbone breakage) between DNA topoisomerase I and DNA.
	GO:0003690	double-stranded DNA binding	Interacting selectively and non-covalently with double-stranded DNA.
	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:0004518	nuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids.
	GO:0008081	phosphoric diester hydrolase activity	Catalysis of the hydrolysis of a phosphodiester to give a phosphomonoester and a free hydroxyl group.
	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:0003697	single-stranded DNA binding	Interacting selectively and non-covalently with single-stranded DNA.
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: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:0006302	double-strand break repair	The repair of double-strand breaks in DNA via homologous and nonhomologous mechanisms to reform a continuous DNA helix.
	GO:0090305	nucleic acid phosphodiester bond hydrolysis	The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
	GO:0000012	single strand break repair	The repair of single strand breaks in DNA. Repair of such breaks is mediated by the same enzyme systems as are used in base excision repair.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0043231	intracellular membrane-bounded organelle	Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
	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.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Asymmetric Unit
	Complete Structure
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	Ligands, Modified Residues, Ions
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	Sites
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	Cis Peptide Bonds
		Leu A:576 - Pro A:577	[ RasMol ]
		Leu B:576 - Pro B:577	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

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	1nop
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		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
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	TYDP1_HUMAN \| Q9NUW8
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

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		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

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	607250
		Disease Information	:	OMIM

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		Age Related Information	:	GenAge

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		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
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Access by UniProt ID/Accession number
	TYDP1_HUMAN \| Q9NUW8
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	TYDP1_HUMAN \| Q9NUW8	:	1jy1 1mu7 1mu9 1qzq 1rff 1rfi 1rg1 1rg2 1rgt 1rgu 1rh0

1jy1	CRYSTAL STRUCTURE OF HUMAN TYROSYL-DNA PHOSPHODIESTERASE (TDP1)
1mu7	CRYSTAL STRUCTURE OF A HUMAN TYROSYL-DNA PHOSPHODIESTERASE (TDP1)-TUNGSTATE COMPLEX
1mu9	CRYSTAL STRUCTURE OF A HUMAN TYROSYL-DNA PHOSPHODIESTERASE (TDP1)-VANADATE COMPLEX

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (4, 8)

PROSITE Motifs (0, 0)

Exons (15, 30)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 4)

CATH Domains (2, 4)

Pfam Domains (1, 2)

Gene Ontology (17, 17)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File