MolNFT v1 · #71110 · protein + DNA
Crystal structure of a bacterial topoisomerase ib in complex with DNA reveals a secondary DNA binding site
3M4A · Putative type I topoisomerase: “Crystal structure of a bacterial topoisomerase ib in complex with DNA reveals a secondary DNA binding site”. X-ray diffraction, 1 ligand (MG), 5 pockets (best druggability 0.48). MolNFT v1 #71110 on…
- PDB
- 3M4A
- Type
- protein + DNA
- Length
- 328 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative type I topoisomerase; DNA (5'-D(*GP*AP*AP*TP*AP*AP*GP*GP*GP*CP*GP*C)-3'); DNA…
- UniProt
- Q9RWH8
- Ligands
- MG
- Pockets
- 5 · best druggability 0.48
Structure
x-ray diffraction · 3 distinct chains · 56% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative type I topoisomerase | protein | 304 | 56% helix, 13% strand | Q9RWH8 |
| D | DNA (5'-D(*GP*AP*AP*TP*AP*AP*GP*GP*GP*CP*GP*C)-3') | dna | 12 | — | — |
| E | DNA (5'-D(*GP*CP*GP*CP*CP*CP*TP*TP*AP*TP*TP*C)-3') | dna | 12 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 234 | 0.48 | 0.74 | 38 | empty |
| 2 | 114 | 0.40 | 0.75 | 19 | empty |
| 3 | 97 | 0.39 | 0.76 | 21 | empty |
| 4 | 80 | 0.36 | 0.76 | 17 | empty |
| 5 | 51 | 0.28 | 0.75 | 16 | empty |
Interfaces
3 interfaces between chains.
- D–E · 540 Ų buried · 47 hydrogen bonds · nucleic-nucleic
- A–D · 434 Ų buried · 11 hydrogen bonds · protein-nucleic
- A–E · 231 Ų buried · 2 hydrogen bonds · protein-nucleic
Compared structures
- 3M4A · Crystal structure of a bacterial topoisomerase IB in complex with DNA reveals a secondary… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q9RWH8
- Elsewhere: RCSB PDB 3M4A · PDBe 3M4A · UniProt Q9RWH8
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