Research workbench
Crystal structure of DNAT84-153-DT10 ssdna complex reveals a novel single-stranded DNA binding mode
Analyse Crystal structure of DNAT84-153-DT10 ssdna complex reveals a novel… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4OU7
- Type
- protein + DNA
- Length
- 364 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Primosomal protein 1; DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
- UniProt
- P0A8J2
- Pockets
- 4 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 52% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E | Primosomal protein 1 | protein | 71 | 54% helix, 6% strand | P0A8J2 |
| C | Primosomal protein 1 | protein | 70 | 51% helix, 6% strand | P0A8J2 |
| S | DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3') | dna | 10 | — | — |
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 305 | 0.65 | 0.81 | 39 | empty |
| 2 | 219 | 0.65 | 0.83 | 29 | empty |
| 3 | 264 | 0.62 | 0.80 | 25 | empty |
| 4 | 208 | 0.61 | 0.82 | 32 | empty |
Interfaces
9 interfaces between chains.
- C–S · 423 Ų buried · 6 hydrogen bonds · protein-nucleic
- C–E · 404 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 382 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 380 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 371 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4OU7 · Crystal structure of DnaT84-153-dT10 ssDNA complex reveals a novel single-stranded DNA… · the same entry in another collection · chain S against S, TM-score 1.00
- P0A8J2 · AlphaFold monomer V2.0 prediction for primosomal protein 1 (P0A8J2) · a predicted model of the same protein · chain B 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 P0A8J2
- Elsewhere: RCSB PDB 4OU7 · PDBe 4OU7 · UniProt P0A8J2
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