2XNK - 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)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   STRUCTURE AND FUNCTION OF THE RAD9-BINDING REGION OF THE DNA DAMAGE CHECKPOINT ADAPTOR TOPBP1

Authors :   M. Rappas, A. W. Oliver, L. H. Pearl

Date :   03 Aug 10 (Deposition) - 01 Sep 10 (Release) - 16 Feb 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)

Keywords :   Isomerase, Phosphorylation, Protein-Protein Interaction, Dna Repair (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Rappas, A. W. Oliver, L. H. Pearl
Structure And Function Of The Rad9-Binding Region Of The Dna-Damage Checkpoint Adaptor Topbp1.
Nucleic Acids Res. V. 39 313 2011
PubMed-ID: 20724438 | Reference-DOI: 10.1093/NAR/GKQ743

Molecule 1 - DNA TOPOISOMERASE 2-BINDING PROTEIN 1
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	POPINH8 AND PGEX6P1
	Expression System Strain	:	ROSETTA2(DE3)PLYSS
	Expression System Taxid	:	562
	Fragment	:	BRCT 0,1 AND 2, RESIDUES 1-290
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	DNA TOPOISOMERASE II-BINDING PROTEIN 1, DNA TOPOISOMERASE II-BETA-BINDING PROTEIN 1, TOPBP1

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 47)

No.	Name	Count	Type	Full Name
1	GOL	11	Ligand/Ion	GLYCEROL
2	MSE	36	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (2, 11)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	MSE	9	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (2, 12)

No.	Name	Count	Type	Full Name
1	GOL	3	Ligand/Ion	GLYCEROL
2	MSE	9	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 3 (2, 12)

No.	Name	Count	Type	Full Name
1	GOL	3	Ligand/Ion	GLYCEROL
2	MSE	9	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 4 (2, 12)

No.	Name	Count	Type	Full Name
1	GOL	3	Ligand/Ion	GLYCEROL
2	MSE	9	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (11, 11)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	LEU A:162 , ASN B:161 , GLN B:277 , ASP B:278 , HOH B:2092	BINDING SITE FOR RESIDUE GOL B1289
02	AC2	SOFTWARE	ASN C:161 , PHE C:275 , GLN C:277 , ASP C:278 , VAL D:158	BINDING SITE FOR RESIDUE GOL C1289
03	AC3	SOFTWARE	VAL C:158 , ASN C:161 , LEU C:162 , ASN D:161 , GLN D:277 , ASP D:278 , ILE D:281	BINDING SITE FOR RESIDUE GOL D1289
04	AC4	SOFTWARE	ALA D:159 , ALA D:160 , LYS D:163 , LYS D:164 , ILE D:166 , PHE D:275 , HOH D:2042	BINDING SITE FOR RESIDUE GOL D1290
05	AC5	SOFTWARE	ASN A:161 , GLN A:277 , ASP A:278 , ILE A:281 , HOH A:2081	BINDING SITE FOR RESIDUE GOL A1290
06	AC6	SOFTWARE	LYS C:72 , PRO C:100 , MSE C:130	BINDING SITE FOR RESIDUE GOL C1290
07	AC7	SOFTWARE	HIS A:240 , HIS A:260 , GLU A:279 , HOH A:2082	BINDING SITE FOR RESIDUE GOL A1291
08	AC8	SOFTWARE	PHE B:9 , PHE B:10 , ARG B:55 , GLN D:232	BINDING SITE FOR RESIDUE GOL B1290
09	AC9	SOFTWARE	TYR D:251 , VAL D:259 , HIS D:260 , CYS D:261 , LYS D:283 , THR D:284 , GLU D:285 , HOH D:2090	BINDING SITE FOR RESIDUE GOL D1291
10	BC1	SOFTWARE	LYS B:12 , GLY D:248 , GLN D:249 , GLU D:252	BINDING SITE FOR RESIDUE GOL B1291
11	BC2	SOFTWARE	CYS C:113 , THR C:114 , SER C:115 , LEU C:116 , ARG C:121 , HOH C:2043	BINDING SITE FOR RESIDUE GOL C1291

Asymmetric Unit

No.	Residues
1	B:206	-	B:238

Asymmetric Unit

No.	Residues
1	Asp A:61	-	Pro A:62
2	Asp B:61	-	Pro B:62
3	Asp C:61	-	Pro C:62
4	Asp D:61	-	Pro D:62

(no "SAP(SNP)/Variant" information available for 2XNK)

Asymmetric Unit (1, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BRCT	PS50172	BRCT domain profile.	TOPB1_HUMAN	101-172 195-284 354-444 548-633 641-738 900-991 1259-1351	8	A:101-172 B:101-172 C:101-172 D:101-172 A:195-284 B:195-284 C:195-284 D:195-284 - - - - -

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BRCT	PS50172	BRCT domain profile.	TOPB1_HUMAN	101-172 195-284 354-444 548-633 641-738 900-991 1259-1351	2	A:101-172 - - - A:195-284 - - - - - - - -

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BRCT	PS50172	BRCT domain profile.	TOPB1_HUMAN	101-172 195-284 354-444 548-633 641-738 900-991 1259-1351	2	- B:101-172 - - - B:195-284 - - - - - - -

Biological Unit 3 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BRCT	PS50172	BRCT domain profile.	TOPB1_HUMAN	101-172 195-284 354-444 548-633 641-738 900-991 1259-1351	2	- - C:101-172 - - - C:195-284 - - - - - -

Biological Unit 4 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BRCT	PS50172	BRCT domain profile.	TOPB1_HUMAN	101-172 195-284 354-444 548-633 641-738 900-991 1259-1351	2	- - - D:101-172 - - - D:195-284 - - - - -

Asymmetric Unit (6, 24)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000260810	1	ENSE00001289464	chr3:133380737-133380613	125	TOPB1_HUMAN	-	0	0	-	-
1.2	ENST00000260810	2	ENSE00000933924	chr3:133379978-133379888	91	TOPB1_HUMAN	1-28	28	4	A:1-28 B:1-28 C:1-28 D:1-28	28 28 28 28
1.3	ENST00000260810	3	ENSE00001018318	chr3:133377994-133377860	135	TOPB1_HUMAN	29-73	45	4	A:29-73 B:29-73 C:29-73 D:29-73	45 45 45 45
1.4	ENST00000260810	4	ENSE00000933926	chr3:133376785-133376642	144	TOPB1_HUMAN	74-121	48	4	A:74-121 B:74-121 C:74-121 D:74-121	48 48 48 48
1.5a	ENST00000260810	5a	ENSE00000933927	chr3:133375701-133375520	182	TOPB1_HUMAN	122-182	61	4	A:122-182 B:122-182 C:122-182 D:122-182	61 61 61 61
1.6	ENST00000260810	6	ENSE00001078162	chr3:133374330-133374134	197	TOPB1_HUMAN	182-248	67	4	A:182-248 B:182-248 C:182-248 D:182-248	67 67 67 67
1.7	ENST00000260810	7	ENSE00001078164	chr3:133372368-133372189	180	TOPB1_HUMAN	248-308	61	4	A:248-289 B:248-288 C:248-288 D:248-288	42 41 41 41
1.8a	ENST00000260810	8a	ENSE00001289360	chr3:133371473-133371307	167	TOPB1_HUMAN	308-363	56	0	-	-
1.9b	ENST00000260810	9b	ENSE00001289349	chr3:133368787-133368624	164	TOPB1_HUMAN	364-418	55	0	-	-
1.9d	ENST00000260810	9d	ENSE00001289339	chr3:133368477-133368227	251	TOPB1_HUMAN	418-502	85	0	-	-
1.10c	ENST00000260810	10c	ENSE00001078161	chr3:133363207-133362864	344	TOPB1_HUMAN	502-616	115	0	-	-
1.11	ENST00000260810	11	ENSE00000933934	chr3:133362216-133362044	173	TOPB1_HUMAN	617-674	58	0	-	-
1.12	ENST00000260810	12	ENSE00001078166	chr3:133359014-133358803	212	TOPB1_HUMAN	674-745	72	0	-	-
1.13	ENST00000260810	13	ENSE00001150558	chr3:133357006-133356720	287	TOPB1_HUMAN	745-840	96	0	-	-
1.14a	ENST00000260810	14a	ENSE00001150552	chr3:133347577-133347404	174	TOPB1_HUMAN	841-898	58	0	-	-
1.15a	ENST00000260810	15a	ENSE00000933939	chr3:133347315-133347206	110	TOPB1_HUMAN	899-935	37	0	-	-
1.16	ENST00000260810	16	ENSE00000933940	chr3:133343019-133342896	124	TOPB1_HUMAN	935-976	42	0	-	-
1.17	ENST00000260810	17	ENSE00001078177	chr3:133342301-133342155	147	TOPB1_HUMAN	977-1025	49	0	-	-
1.18	ENST00000260810	18	ENSE00001078179	chr3:133342037-133341935	103	TOPB1_HUMAN	1026-1060	35	0	-	-
1.19	ENST00000260810	19	ENSE00000933943	chr3:133339191-133338999	193	TOPB1_HUMAN	1060-1124	65	0	-	-
1.20a	ENST00000260810	20a	ENSE00001289481	chr3:133337277-133337057	221	TOPB1_HUMAN	1124-1198	75	0	-	-
1.21b	ENST00000260810	21b	ENSE00000933945	chr3:133336170-133336004	167	TOPB1_HUMAN	1198-1253	56	0	-	-
1.22b	ENST00000260810	22b	ENSE00000933946	chr3:133335769-133335658	112	TOPB1_HUMAN	1254-1291	38	0	-	-
1.23	ENST00000260810	23	ENSE00000933947	chr3:133331396-133331233	164	TOPB1_HUMAN	1291-1345	55	0	-	-
1.24	ENST00000260810	24	ENSE00000933948	chr3:133329985-133329848	138	TOPB1_HUMAN	1346-1391	46	0	-	-
1.25	ENST00000260810	25	ENSE00000933949	chr3:133327806-133327717	90	TOPB1_HUMAN	1392-1421	30	0	-	-
1.26	ENST00000260810	26	ENSE00001150487	chr3:133327540-133327379	162	TOPB1_HUMAN	1422-1475	54	0	-	-
1.27	ENST00000260810	27	ENSE00001289455	chr3:133320237-133319417	821	TOPB1_HUMAN	1476-1522	47	0	-	-

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:291
 aligned with TOPB1_HUMAN | Q92547 from UniProtKB/Swiss-Prot  Length:1522

    Alignment length:291
                              1                                                                                                                                                                                                                                                                                                
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288 
          TOPB1_HUMAN     - --MSRNDKEPFFVKFLKSSDNSKCFFKALESIKEFQSEEYLQIITEEEALKIKENDRSLYICDPFSGVVFDHLKKLGCRIVGPQVVIFCMHHQRCVPRAEHPVYNMVMSDVTISCTSLEKEKREEVHKYVQMMGGRVYRDLNVSVTHLIAGEVGSKKYLVAANLKKPILLPSWIKTLWEKSQEKKITRYTDINMEDFKCPIFLGCIICVTGLCGLDRKEVQQLTVKHGGQYMGQLKMNECTHLIVQEPKGQKYECAKRWNVHCVTTQWFFDSIEKGFCQDESIYKTEPRPE 289
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeee.....hhhhhhhhhhhh...hhh.eeeehhhhhhhh......eee.....hhhhhhhhhhh..eehhhhhhhhhhh...................eeeee..hhhhhhhhhhhhhhh..ee.........eeee....hhhhhhhhhh...ee.hhhhhhhhhhhhh.........hhhhh........eeee...hhhhhhhhhhhhhhh..ee..........eee.....hhhhhhhhhh..eeehhhhhhhhhhhh...hhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------BRCT  PDB: A:101-172 UniProt: 101-172                                   ----------------------BRCT  PDB: A:195-284 UniProt: 195-284                                                     ----- PROSITE
           Transcript 1 (1) --Exon 1.2  PDB: A:1-28       Exon 1.3  PDB: A:29-73 UniProt: 29-73        Exon 1.4  PDB: A:74-121 UniProt: 74-121         Exon 1.5a  PDB: A:122-182 UniProt: 122-182                   -----------------------------------------------------------------Exon 1.7  PDB: A:248-289 UniProt: 248-308  Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.6  PDB: A:182-248 UniProt: 182-248                          ----------------------------------------- Transcript 1 (2)
                 2xnk A  -1 GPmSRNDKEPFFVKFLKSSDNSKCFFKALESIKEFQSEEYLQIITEEEALKIKENDRSLYICDPFSGVVFDHLKKLGCRIVGPQVVIFCmHHQRCVPRAEHPVYNmVmSDVTISCTSLEKEKREEVHKYVQmmGGRVYRDLNVSVTHLIAGEVGSKKYLVAANLKKPILLPSWIKTLWEKSQEKKITRYTDINmEDFKCPIFLGCIICVTGLCGLDRKEVQQLTVKHGGQYmGQLKmNECTHLIVQEPKGQKYECAKRWNVHCVTTQWFFDSIEKGFCQDESIYKTEPRPE 289
                              |      8        18        28        38        48        58        68        78        88        98     | 108       118       128 ||    138       148       158       168       178       188   |   198       208       218       228 |    |238       248       258       268       278       288 
                              |                                                                                     88-MSE         104-MSE                   130-MSE                                                       192-MSE                               230-MSE|                                                      
                              1-MSE                                                                                                  106-MSE                  131-MSE                                                                                                 235-MSE

Chain B from PDB  Type:PROTEIN  Length:290
 aligned with TOPB1_HUMAN | Q92547 from UniProtKB/Swiss-Prot  Length:1522

    Alignment length:290
                              1                                                                                                                                                                                                                                                                                               
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288
          TOPB1_HUMAN     - --MSRNDKEPFFVKFLKSSDNSKCFFKALESIKEFQSEEYLQIITEEEALKIKENDRSLYICDPFSGVVFDHLKKLGCRIVGPQVVIFCMHHQRCVPRAEHPVYNMVMSDVTISCTSLEKEKREEVHKYVQMMGGRVYRDLNVSVTHLIAGEVGSKKYLVAANLKKPILLPSWIKTLWEKSQEKKITRYTDINMEDFKCPIFLGCIICVTGLCGLDRKEVQQLTVKHGGQYMGQLKMNECTHLIVQEPKGQKYECAKRWNVHCVTTQWFFDSIEKGFCQDESIYKTEPRP 288
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeee.....hhhhhhhhhhhhhhhhhh.eeeehhhhhhhh......eee.....hhhhhhhhhhh.eeehhhhhhhhhhhh..................eeeee..hhhhhhhhhhhhhhh..ee.........eeee....hhhhhhhhhh...ee.hhhhhhhhhhhhh....hhhhh.hhhh........eeee...hhhhhhhhhhhhhhh..ee..........eee.....hhhhhhhhhh..eeehhhhhhhhhhhh...hhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------BRCT  PDB: B:101-172 UniProt: 101-172                                   ----------------------BRCT  PDB: B:195-284 UniProt: 195-284                                                     ---- PROSITE
           Transcript 1 (1) --Exon 1.2  PDB: B:1-28       Exon 1.3  PDB: B:29-73 UniProt: 29-73        Exon 1.4  PDB: B:74-121 UniProt: 74-121         Exon 1.5a  PDB: B:122-182 UniProt: 122-182                   -----------------------------------------------------------------Exon 1.7  PDB: B:248-288 UniProt: 248-308 Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.6  PDB: B:182-248 UniProt: 182-248                          ---------------------------------------- Transcript 1 (2)
                 2xnk B  -1 GPmSRNDKEPFFVKFLKSSDNSKCFFKALESIKEFQSEEYLQIITEEEALKIKENDRSLYICDPFSGVVFDHLKKLGCRIVGPQVVIFCmHHQRCVPRAEHPVYNmVmSDVTISCTSLEKEKREEVHKYVQmmGGRVYRDLNVSVTHLIAGEVGSKKYLVAANLKKPILLPSWIKTLWEKSQEKKITRYTDINmEDFKCPIFLGCIICVTGLCGLDRKEVQQLTVKHGGQYmGQLKmNECTHLIVQEPKGQKYECAKRWNVHCVTTQWFFDSIEKGFCQDESIYKTEPRP 288
                              |      8        18        28        38        48        58        68        78        88        98     | 108       118       128 ||    138       148       158       168       178       188   |   198       208       218       228 |    |238       248       258       268       278       288
                              1-MSE                                                                                 88-MSE         104-MSE                   130-MSE                                                       192-MSE                               230-MSE|                                                     
                                                                                                                                     106-MSE                  131-MSE                                                                                                 235-MSE

Chain C from PDB  Type:PROTEIN  Length:289
 aligned with TOPB1_HUMAN | Q92547 from UniProtKB/Swiss-Prot  Length:1522

    Alignment length:289
                             1                                                                                                                                                                                                                                                                                               
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279         
          TOPB1_HUMAN     - -MSRNDKEPFFVKFLKSSDNSKCFFKALESIKEFQSEEYLQIITEEEALKIKENDRSLYICDPFSGVVFDHLKKLGCRIVGPQVVIFCMHHQRCVPRAEHPVYNMVMSDVTISCTSLEKEKREEVHKYVQMMGGRVYRDLNVSVTHLIAGEVGSKKYLVAANLKKPILLPSWIKTLWEKSQEKKITRYTDINMEDFKCPIFLGCIICVTGLCGLDRKEVQQLTVKHGGQYMGQLKMNECTHLIVQEPKGQKYECAKRWNVHCVTTQWFFDSIEKGFCQDESIYKTEPRP 288
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeee.....hhhhhhhhhhhhhhhhhh.eeeehhhhhhhh......eeee....hhhhhhhhhhh.eeehhhhhhhhhhh...................eeeee..hhhhhhhhhhhhhh...ee.........eeee....hhhhhhhhhh...ee.hhhhhhhhhhhhh....hhhhh.hhhh........eeee...hhhhhhhhhhhhhhh..ee..........eee.....hhhhhhhh....eeehhhhhhhhhhhh...hhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------BRCT  PDB: C:101-172 UniProt: 101-172                                   ----------------------BRCT  PDB: C:195-284 UniProt: 195-284                                                     ---- PROSITE
           Transcript 1 (1) -Exon 1.2  PDB: C:1-28       Exon 1.3  PDB: C:29-73 UniProt: 29-73        Exon 1.4  PDB: C:74-121 UniProt: 74-121         Exon 1.5a  PDB: C:122-182 UniProt: 122-182                   -----------------------------------------------------------------Exon 1.7  PDB: C:248-288 UniProt: 248-308 Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.6  PDB: C:182-248 UniProt: 182-248                          ---------------------------------------- Transcript 1 (2)
                 2xnk C   0 PmSRNDKEPFFVKFLKSSDNSKCFFKALESIKEFQSEEYLQIITEEEALKIKENDRSLYICDPFSGVVFDHLKKLGCRIVGPQVVIFCmHHQRCVPRAEHPVYNmVmSDVTISCTSLEKEKREEVHKYVQmmGGRVYRDLNVSVTHLIAGEVGSKKYLVAANLKKPILLPSWIKTLWEKSQEKKITRYTDINmEDFKCPIFLGCIICVTGLCGLDRKEVQQLTVKHGGQYmGQLKmNECTHLIVQEPKGQKYECAKRWNVHCVTTQWFFDSIEKGFCQDESIYKTEPRP 288
                             |       9        19        29        39        49        59        69        79        89        99    | |109       119       129||     139       149       159       169       179       189  |    199       209       219       229|    | 239       249       259       269       279         
                             1-MSE                                                                                 88-MSE         104-MSE                   130-MSE                                                       192-MSE                               230-MSE|                                                     
                                                                                                                                    106-MSE                  131-MSE                                                                                                 235-MSE

Chain D from PDB  Type:PROTEIN  Length:290
 aligned with TOPB1_HUMAN | Q92547 from UniProtKB/Swiss-Prot  Length:1522

    Alignment length:290
                              1                                                                                                                                                                                                                                                                                               
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288
          TOPB1_HUMAN     - --MSRNDKEPFFVKFLKSSDNSKCFFKALESIKEFQSEEYLQIITEEEALKIKENDRSLYICDPFSGVVFDHLKKLGCRIVGPQVVIFCMHHQRCVPRAEHPVYNMVMSDVTISCTSLEKEKREEVHKYVQMMGGRVYRDLNVSVTHLIAGEVGSKKYLVAANLKKPILLPSWIKTLWEKSQEKKITRYTDINMEDFKCPIFLGCIICVTGLCGLDRKEVQQLTVKHGGQYMGQLKMNECTHLIVQEPKGQKYECAKRWNVHCVTTQWFFDSIEKGFCQDESIYKTEPRP 288
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------BRCT-2xnkD01 D:195-271                                                       ----------------- Pfam domains (1)
           Pfam domains (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------BRCT-2xnkD02 D:195-271                                                       ----------------- Pfam domains (2)
           Pfam domains (3) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------BRCT-2xnkD03 D:195-271                                                       ----------------- Pfam domains (3)
           Pfam domains (4) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------BRCT-2xnkD04 D:195-271                                                       ----------------- Pfam domains (4)
           Pfam domains (5) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------BRCT-2xnkD05 D:195-271                                                       ----------------- Pfam domains (5)
           Pfam domains (6) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------BRCT-2xnkD06 D:195-271                                                       ----------------- Pfam domains (6)
           Pfam domains (7) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------BRCT-2xnkD07 D:195-271                                                       ----------------- Pfam domains (7)
           Pfam domains (8) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------BRCT-2xnkD08 D:195-271                                                       ----------------- Pfam domains (8)
         Sec.struct. author ............eeee.....hhhhhhhhhhhhhhh.....eeehhhhhhhh......eee.....hhhhhhhhhh..eeehhhhhhhhhhh...................eeeee..hhhhhhhhhhhhhhh..ee.........eeee....hhhhhhhhhh...ee.hhhhhhhhhhhhh.........hhhhh........eeee...hhhhhhhhhhhhhhh..ee..........eee.....hhhhhhhhhh..eeehhhhhhhhhhhh...hhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------BRCT  PDB: D:101-172 UniProt: 101-172                                   ----------------------BRCT  PDB: D:195-284 UniProt: 195-284                                                     ---- PROSITE
           Transcript 1 (1) --Exon 1.2  PDB: D:1-28       Exon 1.3  PDB: D:29-73 UniProt: 29-73        Exon 1.4  PDB: D:74-121 UniProt: 74-121         Exon 1.5a  PDB: D:122-182 UniProt: 122-182                   -----------------------------------------------------------------Exon 1.7  PDB: D:248-288 UniProt: 248-308 Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.6  PDB: D:182-248 UniProt: 182-248                          ---------------------------------------- Transcript 1 (2)
                 2xnk D  -1 GPmSRNDKEPFFVKFLKSSDNSKCFFKALESIKEFQSEEYLQIITEEEALKIKENDRSLYICDPFSGVVFDHLKKLGCRIVGPQVVIFCmHHQRCVPRAEHPVYNmVmSDVTISCTSLEKEKREEVHKYVQmmGGRVYRDLNVSVTHLIAGEVGSKKYLVAANLKKPILLPSWIKTLWEKSQEKKITRYTDINmEDFKCPIFLGCIICVTGLCGLDRKEVQQLTVKHGGQYmGQLKmNECTHLIVQEPKGQKYECAKRWNVHCVTTQWFFDSIEKGFCQDESIYKTEPRP 288
                              |      8        18        28        38        48        58        68        78        88        98     | 108       118       128 ||    138       148       158       168       178       188   |   198       208       218       228 |    |238       248       258       268       278       288
                              1-MSE                                                                                 88-MSE         104-MSE                   130-MSE                                                       192-MSE                               230-MSE|                                                     
                                                                                                                                     106-MSE                  131-MSE                                                                                                 235-MSE

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 2XNK)

(no "CATH Domain" information available for 2XNK)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: BRCT-like (38)

Family: BRCT (35)

Homo sapiens (Human) (27)

1a	BRCT-2xnkD01	D:195-271
1b	BRCT-2xnkD02	D:195-271
1c	BRCT-2xnkD03	D:195-271
1d	BRCT-2xnkD04	D:195-271
1e	BRCT-2xnkD05	D:195-271
1f	BRCT-2xnkD06	D:195-271
1g	BRCT-2xnkD07	D:195-271
1h	BRCT-2xnkD08	D:195-271

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (TOPB1_HUMAN | Q92547)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0008022	protein C-terminus binding	Interacting selectively and non-covalently with a protein C-terminus, the end of any peptide chain at which the 1-carboxy function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
	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).
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: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:0006260	DNA replication	The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
	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:1901796	regulation of signal transduction by p53 class mediator	Any process that modulates the frequency, rate or extent of signal transduction by p53 class mediator.
	GO:0010212	response to ionizing radiation	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays.
cellular component
	GO:0005794	Golgi apparatus	A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
	GO:0016605	PML body	A class of nuclear body; they react against SP100 auto-antibodies (PML, promyelocytic leukemia); cells typically contain 10-30 PML bodies per nucleus; alterations in the localization of PML bodies occurs after viral infection.
	GO:0015629	actin cytoskeleton	The part of the cytoskeleton (the internal framework of a cell) composed of actin and associated proteins. Includes actin cytoskeleton-associated complexes.
	GO:0005813	centrosome	A structure comprised of a core structure (in most organisms, a pair of centrioles) and peripheral material from which a microtubule-based structure, such as a spindle apparatus, is organized. Centrosomes occur close to the nucleus during interphase in many eukaryotic cells, though in animal cells it changes continually during the cell-division cycle.
	GO:0005694	chromosome	A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
	GO:0000794	condensed nuclear chromosome	A highly compacted molecule of DNA and associated proteins resulting in a cytologically distinct nuclear chromosome.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005856	cytoskeleton	Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
	GO:0001673	male germ cell nucleus	The nucleus of a male germ cell, a reproductive cell in males.
	GO:0005815	microtubule organizing center	An intracellular structure that can catalyze gamma-tubulin-dependent microtubule nucleation and that can anchor microtubules by interacting with their minus ends, plus ends or sides.
	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.
	GO:0000922	spindle pole	Either of the ends of a spindle, where spindle microtubules are organized; usually contains a microtubule organizing center and accessory molecules, spindle microtubules and astral microtubules.

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	2xnk
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	TOPB1_HUMAN \| Q92547	:	1wf6 2xnh 3al2 3al3 3jve 3olc 3pd7 3uen 3ueo

1wf6	THE THIRD BRCA1 C-TERMINUS (BRCT) DOMAIN OF SIMILAR TOS.POMBE RAD4+/CUT5+ PRODUCT
2xnh	STRUCTURE AND FUNCTION OF THE RAD9-BINDING REGION OF THE DNA DAMAGE CHECKPOINT ADAPTOR TOPBP1

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 47)

Sites (11, 11)

SS Bonds (1, 1)

Cis Peptide Bonds (4, 4)

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Exons (6, 24)

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