MolNFT v1 · #57380 · protein + DNA
Promiscuity and specificity in DNA binding to ssb: insights from the structure of the mycobacterium smegmatis ssb-ssdna complex
3A5U · Single-stranded DNA-binding protein: “Promiscuity and specificity in DNA binding to ssb: insights from the structure of the mycobacterium smegmatis…”. X-ray diffraction, 4 pockets (best druggability 0.56). MolNFT v1 #57380 on…
- PDB
- 3A5U
- Type
- protein + DNA
- Length
- 256 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Single-stranded DNA-binding protein; DNA (31-mer)
- UniProt
- Q9AFI5
- Pockets
- 4 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Single-stranded DNA-binding protein | protein | 118 | 8% helix, 43% strand | Q9AFI5 |
| B | Single-stranded DNA-binding protein | protein | 112 | 9% helix, 49% strand | Q9AFI5 |
| C | DNA (31-mer) | dna | 26 | — | — |
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 274 | 0.56 | 0.77 | 33 | empty |
| 2 | 250 | 0.51 | 0.75 | 29 | empty |
| 3 | 116 | 0.43 | 0.77 | 16 | empty |
| 4 | 116 | 0.38 | 0.74 | 20 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1833 Ų buried · 38 hydrogen bonds · protein-nucleic
- A–C · 1189 Ų buried · 18 hydrogen bonds · protein-nucleic
- A–B · 1078 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 3A5U · Promiscuity and specificity in DNA binding to SSB: Insights from the structure of the… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9AFI5 · AlphaFold monomer V2.0 prediction for single-stranded DNA-binding protein (Q9AFI5) · a predicted model of the same protein · chain B against A, TM-score 0.94
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 Q9AFI5
- Elsewhere: RCSB PDB 3A5U · PDBe 3A5U · UniProt Q9AFI5
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