Research workbench
Structure of a single-stranded DNA-binding protein (ssb), from coxiella burnetii
Analyse Structure of a single-stranded DNA-binding protein (ssb), from coxiella burnetii in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TQY
- Type
- protein
- Length
- 425 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Single-stranded DNA-binding protein
- EC
- 2.7.7.6
- UniProt
- Q83EP4
- Pockets
- 5 · best druggability 0.54
Structure
x-ray diffraction · 4 distinct chains · 9% helix, 63% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Single-stranded DNA-binding protein (EC 2.7.7.6) | protein | 110 | 8% helix, 63% strand | Q83EP4 |
| B | Single-stranded DNA-binding protein (EC 2.7.7.6) | protein | 109 | 9% helix, 61% strand | Q83EP4 |
| C | Single-stranded DNA-binding protein (EC 2.7.7.6) | protein | 108 | 9% helix, 64% strand | Q83EP4 |
| D | Single-stranded DNA-binding protein (EC 2.7.7.6) | protein | 98 | 10% helix, 62% strand | Q83EP4 |
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 202 | 0.54 | 0.78 | 31 | empty |
| 2 | 286 | 0.51 | 0.74 | 46 | empty |
| 3 | 55 | 0.40 | 0.81 | 17 | empty |
| 4 | 123 | 0.40 | 0.75 | 20 | empty |
| 5 | 107 | 0.37 | 0.75 | 20 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1685 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 1032 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 374 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 324 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 218 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 9 modified (engineered).
Compared structures
- 3TQY · Structure of a single-stranded DNA-binding protein (ssb), from Coxiella burnetii · the same entry in another collection · chain D against D, TM-score 1.00
- Q83EP4 · AlphaFold monomer V2.0 prediction for single-stranded DNA-binding protein (Q83EP4) · a predicted model of the same protein · chain D against A, TM-score 0.96
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 Q83EP4
- Elsewhere: RCSB PDB 3TQY · PDBe 3TQY · UniProt Q83EP4
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