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Crystal structure of mthsbds, the homologue of the shwachman-bodian- diamond syndrome protein in the euriarchaeon methanothermobacter thermautotrophicus
Analyse Crystal structure of mthsbds, the homologue of the shwachman-bodian- diamond… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2WBM
- Type
- protein
- Length
- 461 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribosome maturation protein SDO1 homolog
- UniProt
- O26781
- Ligands
- SO4, CL
- Pockets
- 2 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribosome maturation protein SDO1 homolog | protein | 234 | 44% helix, 23% strand | O26781 |
| B | Ribosome maturation protein SDO1 homolog | protein | 227 | 45% helix, 24% strand | O26781 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains B
- CL · Chloride ion · ion · chains B
- GOL · Glycerol · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 827 | 0.69 | 0.75 | 56 | empty |
| 2 | 54 | 0.31 | 0.76 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 207 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 2WBM · Crystal structure of mthSBDS, the homologue of the Shwachman-Bodian- Diamond syndrome… · the same entry in another collection · chain A against A, TM-score 1.00
- O26781 · AlphaFold monomer V2.0 prediction for ribosome maturation protein SDO1 homolog (O26781) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 O26781
- Elsewhere: RCSB PDB 2WBM · PDBe 2WBM · UniProt O26781
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