Research workbench
Structure of mycobacterium tuberculosis dnaa-dbd in complex with BOX1 DNA
Analyse Structure of mycobacterium tuberculosis dnaa-dbd in complex with BOX1 DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PVV
- Type
- protein + DNA
- Length
- 243 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chromosomal replication initiator protein dnaa; DNA…
- UniProt
- A5TY69
- Pockets
- 7 · best druggability 0.60
Structure
x-ray diffraction · 4 distinct chains · 78% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chromosomal replication initiator protein dnaa | protein | 96 | 78% helix, 0% strand | A5TY69 |
| B | Chromosomal replication initiator protein dnaa | protein | 95 | 78% helix, 0% strand | A5TY69 |
| C, E | DNA (5'-D(*CP*GP*TP*TP*GP*TP*CP*CP*AP*CP*AP*AP*C)-3') | dna | 13 | — | — |
| D, F | DNA (5'-D(*GP*TP*TP*GP*TP*GP*GP*AP*CP*AP*AP*CP*G)-3') | dna | 13 | — | — |
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 154 | 0.60 | 0.83 | 25 | empty |
| 2 | 214 | 0.57 | 0.79 | 29 | empty |
| 3 | 178 | 0.54 | 0.79 | 26 | empty |
| 4 | 126 | 0.51 | 0.81 | 20 | empty |
| 5 | 95 | 0.49 | 0.82 | 23 | empty |
Interfaces
9 interfaces between chains.
- A–B · 697 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 599 Ų buried · 62 hydrogen bonds · nucleic-nucleic
- E–F · 595 Ų buried · 59 hydrogen bonds · nucleic-nucleic
- A–D · 468 Ų buried · 8 hydrogen bonds · protein-nucleic
- A–C · 467 Ų buried · 13 hydrogen bonds · protein-nucleic
Compared structures
- 3PVV · Structure of Mycobacterium tuberculosis DnaA-DBD in complex with box1 DNA · the same entry in another collection · chain F against F, TM-score 1.00
- A5TY69 · AlphaFold monomer V2.0 prediction for chromosomal replication initiator protein dnaa… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 A5TY69
- Elsewhere: RCSB PDB 3PVV · PDBe 3PVV · UniProt A5TY69
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