Research workbench
Crystal structure of the probable amino-acid ABC transporter extracellular-binding protein ytmk from bacillus subtilis. northeast structural genomics consortium target SR572
Analyse Crystal structure of the probable amino-acid ABC transporter… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2O1M
- Type
- protein
- Length
- 456 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable amino-acid ABC transporter extracellular-binding protein ytmk
- UniProt
- O34852
- Ligands
- SO4
- Pockets
- 3 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable amino-acid ABC transporter extracellular-binding protein ytmk | protein | 232 | 37% helix, 29% strand | O34852 |
| B | Probable amino-acid ABC transporter extracellular-binding protein ytmk | protein | 224 | 38% helix, 27% strand | O34852 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 610 | 0.70 | 0.78 | 44 | empty |
| 2 | 556 | 0.65 | 0.76 | 41 | empty |
| 3 | 56 | 0.27 | 0.73 | 15 | empty |
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 2O1M · Crystal structure of the probable amino-acid ABC transporter extracellular-binding… · the same entry in another collection · chain A against A, TM-score 1.00
- O34852 · AlphaFold monomer V2.0 prediction for L-cystine-binding protein tcyk (O34852) · a predicted model of the same protein · chain B against A, TM-score 0.87
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 O34852
- Elsewhere: RCSB PDB 2O1M · PDBe 2O1M · UniProt O34852
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