2XNK: DNA topoisomerase 2-binding protein 1

Name: PDB 2XNK: Structure and function of the Rad9-binding region of the DNA damage checkpoint adaptor TopBP1
Published: 2010-09-01
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: isomerase

Structure and function of the Rad9-binding region of the DNA damage checkpoint adaptor TopBP1. Determined by X-ray diffraction at 2.6 Å resolution. Released 1 Sept 2010.

Method: X-ray diffraction
Resolution: 2.6 Å
Organism: HOMO SAPIENS
Chains: 4
Atoms: 9,842
Mol. weight: 138.27 kDa
Released: 1 Sept 2010

Explore 2XNK in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2XNK contains 64 α-helices and 60 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 16 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	7-8	2
β-strand	11-14	4	1
α-helix	21-30	10
α-helix	36-38	3
β-strand	39-42	4	1
α-helix	44-49	6
β-strand	57-59	3	1
α-helix	66-74	9
β-strand	78-79	2	1
α-helix	81-89	9
α-helix	93-96	4
β-strand	101	1	1
β-strand	110-114	5	2
α-helix	118-130	13
β-strand	134-135	2	2
β-strand	145-148	4	2
α-helix	154-161	8
β-strand	166-167	2	2
α-helix	170-180	11
α-helix	192-195	4
β-strand	196	1	2
α-helix	197-198	2
β-strand	204-207	4	3
α-helix	212-224	13
β-strand	228-229	2	3
β-strand	240-242	3	3
α-helix	249-256	8
β-strand	260-262	3	3
α-helix	264-273	10
α-helix	279-282	4
β-strand	283	1	3

Chain B: 17 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	11-14	4	4
α-helix	21-33	13
α-helix	36-38	3
β-strand	39-42	4	4
α-helix	44-49	6
α-helix	56	1
β-strand	57-59	3	4
α-helix	66-74	9
β-strand	77-79	3	4
α-helix	81-90	10
α-helix	93-96	4
β-strand	101	1	4
β-strand	110-114	5	5
α-helix	118-130	13
β-strand	134-135	2	5
β-strand	145-148	4	5
α-helix	154-161	8
β-strand	166-167	2	5
α-helix	170-180	11
α-helix	187-189	3
α-helix	193-195	3
β-strand	196	1	5
α-helix	197-198	2
β-strand	204-207	4	6
α-helix	212-224	13
β-strand	228-229	2	6
β-strand	240-242	3	6
α-helix	249-256	8
β-strand	260-262	3	6
α-helix	264-273	10
α-helix	279-282	4
β-strand	283	1	6

Chain C: 16 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	11-14	4	7
α-helix	21-33	13
α-helix	36-38	3
β-strand	39-42	4	7
α-helix	44-49	6
β-strand	57-60	4	7
α-helix	66-74	9
β-strand	77-79	3	7
α-helix	81-89	9
α-helix	93-95	3
β-strand	101	1	7
β-strand	110-114	5	8
α-helix	118-129	12
β-strand	134-135	2	8
β-strand	145-148	4	8
α-helix	154-161	8
β-strand	166-167	2	8
α-helix	170-180	11
α-helix	187-189	3
α-helix	193-195	3
β-strand	196	1	8
α-helix	197-198	2
β-strand	204-208	5	9
α-helix	212-224	13
β-strand	228-229	2	9
β-strand	240-243	4	9
α-helix	249-254	6
β-strand	260-262	3	9
α-helix	264-273	10
α-helix	279-281	3
β-strand	283	1	9

Chain D: 15 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	11-14	4	10
α-helix	21-30	10
α-helix	31-33	3
β-strand	40-42	3	10
α-helix	44-49	6
β-strand	57-59	3	10
α-helix	66-73	8
β-strand	77-79	3	10
α-helix	81-89	9
α-helix	93-96	4
β-strand	101	1	10
β-strand	110-114	5	11
α-helix	118-130	13
β-strand	134-135	2	11
β-strand	145-148	4	11
α-helix	154-161	8
β-strand	166-167	2	11
α-helix	170-180	11
α-helix	192-195	4
β-strand	196	1	11
β-strand	204-208	5	12
α-helix	212-224	13
β-strand	228-229	2	12
β-strand	240-243	4	12
α-helix	249-256	8
β-strand	260-262	3	12
α-helix	264-273	10
α-helix	276-278	3
α-helix	279-282	4
β-strand	283	1	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA topoisomerase 2-binding protein 1	A, B, C, D	protein	292	HOMO SAPIENS	Q92547 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>2XNK_1 DNA TOPOISOMERASE 2-BINDING PROTEIN 1 (chains A, B, C, D)
GPMSRNDKEPFFVKFLKSSDNSKCFFKALESIKEFQSEEYLQIITEEEALKIKENDRSLY
ICDPFSGVVFDHLKKLGCRIVGPQVVIFCMHHQRCVPRAEHPVYNMVMSDVTISCTSLEK
EKREEVHKYVQMMGGRVYRDLNVSVTHLIAGEVGSKKYLVAANLKKPILLPSWIKTLWEK
SQEKKITRYTDINMEDFKCPIFLGCIICVTGLCGLDRKEVQQLTVKHGGQYMGQLKMNEC
THLIVQEPKGQKYECAKRWNVHCVTTQWFFDSIEKGFCQDESIYKTEPRPEA

Primary citation

Structure and Function of the Rad9-Binding Region of the DNA-Damage Checkpoint Adaptor Topbp1. Rappas, M., Oliver, A.W., Pearl, L.H. Nucleic Acids Res (2011) 39:313. DOI 10.1093/NAR/GKQ743 · PubMed

Other PDB entries of the same protein (UniProt Q92547 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3PD7 1.26 Å, Crystal Structure of the Sixth BRCT Domain of Human TopBP1
3JVE 1.34 Å, Crystal Structure of the Sixth BRCT Domain of TopBP1
9MAT 1.65 Å, TopBP1 BRCT 7-8 Domain
7CMZ 1.7 Å, Crystal Structure of BRCT7/8 in Complex with the APS Motif of PHF8
3UEN 1.9 Å, Crystal structure of TopBP1 BRCT4/5 domains
3AL2 2.0 Å, Crystal Structure of TopBP1 BRCT7/8
3AL3 2.15 Å, Crystal Structure of TopBP1 BRCT7/8-BACH1 peptide complex
3OLC 2.4 Å, Crystal structure of the N-terminal region of TopBP1
9MAW 2.45 Å, Crystal structure of TOPBP1BRCT7-8 domain in complex with 1-Adamantaneacetic acid
3UEO 2.6 Å, Crystal structure of TopBP1 BRCT4/5 domains in complex with a phospho-peptide
2XNH 2.8 Å, Structure and function of the Rad9-binding region of the DNA damage checkpoint adaptor…
6RML 2.81 Å, Crystal structure of TOPBP1 BRCT0,1,2 in complex with a 53BP1 phosphopeptide

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