Research workbench
Crystal structure of E.COLI sbcd with MN2+
Analyse Crystal structure of E.COLI sbcd with MN2+ in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4M0V
- Type
- protein
- Length
- 1,364 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Exonuclease subunit sbcd
- UniProt
- E8Y9D8
- Ligands
- MN
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Exonuclease subunit sbcd | protein | 332 | 29% helix, 27% strand | E8Y9D8 |
| B | Exonuclease subunit sbcd | protein | 342 | 30% helix, 29% strand | E8Y9D8 |
| C, D | Exonuclease subunit sbcd | protein | 345 | 30% helix, 28% strand | E8Y9D8 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 8 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 72 | 0.75 | 0.98 | 19 | GOL |
| 2 | 571 | 0.75 | 0.82 | 73 | empty |
| 3 | 435 | 0.71 | 0.82 | 52 | empty |
| 4 | 400 | 0.70 | 0.82 | 47 | empty |
| 5 | 387 | 0.68 | 0.81 | 59 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1007 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 695 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 217 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 197 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4M0V · Crystal structure of E.coli SbcD with Mn2+ · the same entry in another collection · chain A against A, 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 4M0V · PDBe 4M0V · UniProt E8Y9D8
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