Research workbench
Crystal structure of dnaa domainiv complexed with dnaabox DNA
Analyse Crystal structure of dnaa domainiv complexed with dnaabox DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1J1V
- Type
- protein + DNA
- Length
- 120 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*TP*GP*TP*TP*AP*TP*CP*CP*AP*CP*AP*GP*G)-3'…
- UniProt
- P03004
- Pockets
- 1 · best druggability 0.37
Structure
x-ray diffraction · 3 distinct chains · 76% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | 5'-D(*TP*GP*TP*TP*AP*TP*CP*CP*AP*CP*AP*GP*G)-3' | dna | 13 | — | — |
| C | 5'-D(*CP*CP*TP*GP*TP*GP*GP*AP*TP*AP*AP*CP*A)-3' | dna | 13 | — | — |
| A | Chromosomal replication initiator protein dnaa | protein | 94 | 76% helix, 0% strand | P03004 |
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 89 | 0.37 | 0.76 | 14 | empty |
Interfaces
3 interfaces between chains.
- B–C · 593 Ų buried · 50 hydrogen bonds · nucleic-nucleic
- C–A · 530 Ų buried · 11 hydrogen bonds · protein-nucleic
- B–A · 521 Ų buried · 9 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (engineered).
Compared structures
- 1J1V · Crystal structure of DnaA domainIV complexed with DnaAbox DNA · the same entry in another collection · chain B against B, TM-score 1.00
- P03004 · 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 P03004
- Elsewhere: RCSB PDB 1J1V · PDBe 1J1V · UniProt P03004
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