Research workbench
Structure of small toprim domain-containing protein from B. stearothermophilus in complex with MG2+
Analyse Structure of small toprim domain-containing protein from B. stearothermophilus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2I5R
- Type
- protein
- Length
- 350 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Toprim domain-containing protein
- Ligands
- MG, SO4
- Pockets
- 3 · best druggability 0.38
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Toprim domain-containing protein | protein | 115 | 43% helix, 17% strand | — |
| B | Toprim domain-containing protein | protein | 118 | 45% helix, 16% strand | — |
| C | Toprim domain-containing protein | protein | 117 | 44% helix, 16% strand | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains C
- GOL · Glycerol · additive · 6 copies · chains A, C, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 100 | 0.38 | 0.76 | 17 | empty |
| 2 | 91 | 0.36 | 0.75 | 14 | empty |
| 3 | 52 | 0.25 | 0.72 | 15 | empty |
Interfaces
2 interfaces between chains.
- A–B · 570 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 512 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 2I5R · Structure of small Toprim domain-containing protein from B. stearothermophilus in complex… · 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
- Elsewhere: RCSB PDB 2I5R · PDBe 2I5R
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