Research workbench
Crystal structure of E.COLI sbcd at 2.5 ångström resolution
Analyse Crystal structure of E.COLI sbcd at 2.5 ångström resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LU9
- Type
- protein
- Length
- 1,365 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Exonuclease subunit sbcd
- UniProt
- E8Y9D8
- Pockets
- 7 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 29% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Exonuclease subunit sbcd | protein | 336 | 29% helix, 27% strand | E8Y9D8 |
| B | Exonuclease subunit sbcd | protein | 342 | 28% helix, 27% strand | E8Y9D8 |
| A | Exonuclease subunit sbcd | protein | 343 | 29% helix, 27% strand | E8Y9D8 |
| D | Exonuclease subunit sbcd | protein | 344 | 30% helix, 27% strand | E8Y9D8 |
Ligands and binding sites
- GOL · Glycerol · additive · 4 copies · chains C, A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 996 | 0.82 | 0.83 | 118 | empty |
| 2 | 83 | 0.77 | 0.98 | 22 | GOL |
| 3 | 393 | 0.70 | 0.82 | 48 | empty |
| 4 | 360 | 0.69 | 0.82 | 43 | empty |
| 5 | 244 | 0.53 | 0.76 | 33 | empty |
Interfaces
4 interfaces between chains.
- A–D · 989 Ų buried · 23 hydrogen bonds · protein-protein
- C–A · 707 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 336 Ų buried · 1 hydrogen bond · protein-protein
- C–B · 297 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4LU9 · Crystal structure of E.coli SbcD at 2.5 angstrom resolution · the same entry in another collection · chain C against C, TM-score 1.00
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 E8Y9D8
- Elsewhere: RCSB PDB 4LU9 · PDBe 4LU9 · UniProt E8Y9D8
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