9MAT: TopBP1 BRCT 7-8 Domain

TopBP1 BRCT 7-8 Domain. Determined by X-ray diffraction at 1.65 Å resolution. Released 18 Mar 2026.

Method: X-ray diffraction
Resolution: 1.65 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,249
Mol. weight: 26.49 kDa
Ligands: MLA
Released: 18 Mar 2026

Explore 9MAT in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9MAT contains 15 α-helices and 10 β-strands across 1 chain. 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: 15 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	1263-1267	5
β-strand	1269-1273	5	1
α-helix	1277-1289	13
β-strand	1293-1294	2	1
β-strand	1306-1309	4	1
α-helix	1316-1323	8
β-strand	1327-1329	3	1
α-helix	1332-1340	9
α-helix	1343-1345	3
α-helix	1347-1349	3
β-strand	1350	1	1
α-helix	1354-1357	4
α-helix	1365-1382	18
α-helix	1385-1386	2
β-strand	1398-1401	4	2
α-helix	1405-1417	13
β-strand	1421-1422	2	2
α-helix	1428-1431	4
β-strand	1436-1439	4	2
α-helix	1453-1458	6
β-strand	1462-1465	4	2
α-helix	1467-1474	8
α-helix	1481-1484	4
β-strand	1485	1	2
α-helix	1487-1491	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA topoisomerase 2-binding protein 1	A	protein	233	Homo sapiens	Q92547 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9MAT_1 DNA topoisomerase 2-binding protein 1 (chains A)
GHMLKKQYIFQLSSLNPQERIDYCHLIEKLGGLVIEKQCFDPTCTHIVVGHPLRNEKYLA
SVAAGKWVLHRSYLEACRTAGHFVQEEDYEWGSSSILDVLTGINVQQRRLALAAMRWRKK
IQQRQESGIVEGAFSGWKVILHVDQSREAGFKRLLQSGGAKVLPGHSVPLFKEATHLFSD
LNKLKPDDSGVNIAEAAAQNVYCLRTEYIADYLMQESPPHVENYCLPEAISFI

Ligands and cofactors

ID	Name	Formula	Copies
MLA	Malonic acid	C3 H4 O4	1

Primary citation

Fragment-based discovery of TopBP1 inhibitors integrated with AI-driven molecular docking. Chen, W., Zhang, S., Li, Z. et al. Magn Reson Lett (2026) 6:200251-200251. DOI 10.1016/j.mrl.2025.200251 · 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
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
2XNK 2.6 Å, Structure and function of the Rad9-binding region of the DNA damage checkpoint adaptor…
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

Browse structure collections

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