Research workbench
Crystal structure of a pduo-type ATP:COB(I)ALAMIN adenosyltransferase from bacillus cereus
Analyse Crystal structure of a pduo-type ATP:COB(I)ALAMIN adenosyltransferase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KE4
- Type
- protein
- Length
- 509 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical cytosolic protein
- EC
- 2.5.1.17
- UniProt
- Q813T7
- Pockets
- 5 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 65% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypothetical cytosolic protein (EC 2.5.1.17) | protein | 172 | 63% helix, 7% strand | Q813T7 |
| B | Hypothetical cytosolic protein (EC 2.5.1.17) | protein | 168 | 65% helix, 8% strand | Q813T7 |
| C | Hypothetical cytosolic protein (EC 2.5.1.17) | protein | 169 | 66% helix, 8% strand | Q813T7 |
Ligands and binding sites
- DIO · 1,4-diethylene dioxide · additive · 8 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 406 | 0.65 | 0.78 | 39 | DIO |
| 2 | 387 | 0.63 | 0.78 | 27 | empty |
| 3 | 348 | 0.62 | 0.78 | 37 | DIO |
| 4 | 342 | 0.60 | 0.77 | 37 | DIO |
| 5 | 54 | 0.43 | 0.83 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1227 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 1158 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 1105 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 3KE4 · Crystal structure of a PduO-Type ATP:Cob(I)alamin adenosyltransferase from Bacillus cereus · 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 Q813T7
- Elsewhere: RCSB PDB 3KE4 · PDBe 3KE4 · UniProt Q813T7
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