Research workbench
EXOI/SSB-ct complex
Analyse EXOI/SSB-ct complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3C94
- Type
- protein
- Length
- 465 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Exodeoxyribonuclease I; Single-stranded DNA-binding C-terminal tail peptide
- EC
- 3.1.11.1
- UniProt
- P04995, P0AGE0
- Ligands
- MG
- Pockets
- 6 · best druggability 0.51
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Exodeoxyribonuclease I (EC 3.1.11.1) | protein | 458 | 50% helix, 14% strand | P04995 |
| B | Single-stranded DNA-binding C-terminal tail peptide | protein | 4 | 0% helix, 0% strand | P0AGE0 |
| C | Single-stranded DNA-binding C-terminal tail peptide | protein | 3 | 0% helix, 0% strand | P0AGE0 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 223 | 0.51 | 0.76 | 22 | empty |
| 2 | 258 | 0.51 | 0.75 | 35 | MG |
| 3 | 250 | 0.50 | 0.75 | 42 | empty |
| 4 | 69 | 0.49 | 0.84 | 25 | empty |
| 5 | 125 | 0.45 | 0.78 | 25 | empty |
Interfaces
2 interfaces between chains.
- A–B · 329 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 274 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3C94 · ExoI/SSB-Ct complex · the same entry in another collection · chain A against A, TM-score 1.00
- P0AGE0 · AlphaFold monomer V2.0 prediction for single-stranded DNA-binding protein (P0AGE0) · a predicted model of the same protein · chain C against A, TM-score 1.00
- P04995 · AlphaFold monomer V2.0 prediction for exodeoxyribonuclease I (P04995) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P04995
- Every structure of UniProt P0AGE0
- Elsewhere: RCSB PDB 3C94 · PDBe 3C94 · UniProt P04995 · UniProt P0AGE0
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