Research workbench
Crystal structure of a pduo-type ATP:COB(I)ALAMIN adenosyltransferase from bacillus cereus in a complex with ATP
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
- 3KE5
- Type
- protein
- Length
- 540 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
- Ligands
- ATP, MG
- Pockets
- 6 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 61% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypothetical cytosolic protein (EC 2.5.1.17) | protein | 182 | 61% helix, 7% strand | Q813T7 |
| B | Hypothetical cytosolic protein (EC 2.5.1.17) | protein | 179 | 61% helix, 7% strand | Q813T7 |
| C | Hypothetical cytosolic protein (EC 2.5.1.17) | protein | 179 | 62% helix, 8% strand | Q813T7 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 3 copies · chains A, C, B
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 554 | 0.71 | 0.80 | 55 | MG, ATP |
| 2 | 50 | 0.70 | 0.98 | 13 | empty |
| 3 | 481 | 0.67 | 0.78 | 50 | MG, ATP |
| 4 | 441 | 0.66 | 0.78 | 49 | ATP, MG |
| 5 | 359 | 0.65 | 0.80 | 28 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1693 Ų buried · 29 hydrogen bonds · protein-protein
- A–C · 1649 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 1566 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 3KE5 · Crystal structure of a PduO-Type ATP:Cob(I)alamin adenosyltransferase from Bacillus… · 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 3KE5 · PDBe 3KE5 · UniProt Q813T7
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