Research workbench
Crystal structure of the single-stranded DNA binding protein from mycobacterium leprae (form II)
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
- 3AFQ
- Type
- protein
- Length
- 430 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Single-stranded DNA-binding protein
- UniProt
- P46390
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 9% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Single-stranded DNA-binding protein | protein | 105 | 10% helix, 55% strand | P46390 |
| B | Single-stranded DNA-binding protein | protein | 113 | 9% helix, 56% strand | P46390 |
| C | Single-stranded DNA-binding protein | protein | 105 | 10% helix, 57% strand | P46390 |
| D | Single-stranded DNA-binding protein | protein | 107 | 9% helix, 56% strand | P46390 |
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 870 | 0.73 | 0.77 | 85 | empty |
| 2 | 118 | 0.38 | 0.74 | 23 | empty |
| 3 | 80 | 0.32 | 0.74 | 12 | empty |
Interfaces
6 interfaces between chains.
- A–D · 1379 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 1376 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1106 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1098 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 108 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3AFQ · Crystal structure of the single-stranded DNA binding protein from Mycobacterium leprae… · the same entry in another collection · chain D against D, TM-score 1.00
- P46390 · AlphaFold monomer V2.0 prediction for single-stranded DNA-binding protein (P46390) · a predicted model of the same protein · chain C against A, TM-score 0.95
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 P46390
- Elsewhere: RCSB PDB 3AFQ · PDBe 3AFQ · UniProt P46390
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