Research workbench
Crystal structure of the cbs domain pair of protein MJ0100 in complex with 5 -methylthioadenosine and S-adenosyl-L- methionine.
Analyse Crystal structure of the cbs domain pair of protein MJ0100 in complex with 5… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KPB
- Type
- protein
- Length
- 476 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein MJ0100
- UniProt
- Q57564
- Ligands
- SAM
- Pockets
- 6 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, B, D | Uncharacterized protein MJ0100 | protein | 119 | 39% helix, 26% strand | Q57564 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 3 copies · chains A, C, D
- GOL · Glycerol · additive · 5 copies · chains C, B, A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 338 | 0.63 | 0.79 | 36 | empty |
| 2 | 442 | 0.63 | 0.77 | 50 | SAM |
| 3 | 294 | 0.53 | 0.75 | 37 | SAM |
| 4 | 93 | 0.43 | 0.79 | 22 | empty |
| 5 | 76 | 0.36 | 0.76 | 18 | empty |
Interfaces
3 interfaces between chains.
- C–D · 838 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 781 Ų buried · 1 hydrogen bond · protein-protein
- C–B · 176 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3KPB · Crystal Structure of the CBS domain pair of protein MJ0100 in complex with 5… · the same entry in another collection · chain D against D, TM-score 1.00
- Q57564 · AlphaFold monomer V2.0 prediction for L-aspartate semialdehyde sulfurtransferase (Q57564) · a predicted model of the same protein · chain A against A, TM-score 0.93
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 Q57564
- Elsewhere: RCSB PDB 3KPB · PDBe 3KPB · UniProt Q57564
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