Research workbench
Crystal structure of the single-stranded DNA-binding protein from mycobacterium smegmatis
Analyse Crystal structure of the single-stranded DNA-binding protein from mycobacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1X3F
- Type
- protein
- Length
- 222 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Single-strand binding protein
- UniProt
- Q9AFI5
- Ligands
- CD
- Pockets
- 2 · best druggability 0.30
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Single-strand binding protein | protein | 107 | 8% helix, 57% strand | Q9AFI5 |
| B | Single-strand binding protein | protein | 115 | 9% helix, 55% strand | Q9AFI5 |
Ligands and binding sites
- CD · Cadmium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 57 | 0.30 | 0.75 | 13 | empty |
| 2 | 57 | 0.26 | 0.73 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 1403 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
- 1X3F · Crystal structure of the single-stranded DNA-binding protein from Mycobacterium SMEGMATIS · 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 1X3F · PDBe 1X3F · UniProt Q9AFI5
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