Research workbench
Human mitochondrial single-stranded DNA binding protein, SSBP1, at 2.1 A resolution - elucidated sequence
Analyse Human mitochondrial single-stranded DNA binding protein, SSBP1, at 2.1 A… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RUP
- Type
- protein
- Length
- 224 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.1
- Source
- Homo sapiens
- Molecule
- Single-stranded DNA-binding protein, mitochondrial; Ser-ser-ser-ser
- UniProt
- Q04837
- Ligands
- MG
- Pockets
- 4 · best druggability 0.43
Structure
x-ray diffraction · resolution 2.1 · 3 distinct chains · 8% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Single-stranded DNA-binding protein, mitochondrial | protein | 111 | 9% helix, 56% strand | Q04837 |
| B | Single-stranded DNA-binding protein, mitochondrial | protein | 109 | 7% helix, 53% strand | Q04837 |
| C | Ser-ser-ser-ser | protein | 4 | 0% helix, 50% strand | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 134 | 0.43 | 0.76 | 22 | empty |
| 2 | 63 | 0.33 | 0.77 | 15 | empty |
| 3 | 56 | 0.26 | 0.73 | 16 | empty |
| 4 | 53 | 0.25 | 0.73 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1518 Ų buried · 37 hydrogen bonds · protein-protein
- A–C · 190 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 66 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6RUP · Human mitochondrial single-stranded DNA binding protein, SSBP1, at 2.1 a resolution… · the same entry in another collection · chain A against A, TM-score 1.00
- Q04837 · AlphaFold monomer V2.0 prediction for single-stranded DNA-binding protein, mitochondrial… · a predicted model of the same protein · chain A against A, TM-score 0.90
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 Q04837
- Elsewhere: RCSB PDB 6RUP · PDBe 6RUP · UniProt Q04837
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