Research workbench
Structure of human ATP:COBALAMIN adenosyltransferase R190C bound to ATP
Analyse Structure of human ATP:COBALAMIN adenosyltransferase R190C bound to ATP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RUT
- Type
- protein
- Length
- 1,117 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Corrinoid adenosyltransferase
- EC
- 2.5.1.17
- UniProt
- Q96EY8
- Ligands
- ATP, K, MG
- Pockets
- 12 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 61% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | Corrinoid adenosyltransferase (EC 2.5.1.17) | protein | 187 | 58% helix, 4% strand | Q96EY8 |
| C, F, A | Corrinoid adenosyltransferase (EC 2.5.1.17) | protein | 186 | 62% helix, 4% strand | Q96EY8 |
| B | Corrinoid adenosyltransferase (EC 2.5.1.17) | protein | 187 | 63% helix, 4% strand | Q96EY8 |
| D | Corrinoid adenosyltransferase (EC 2.5.1.17) | protein | 185 | 61% helix, 4% strand | Q96EY8 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 6 copies · chains E, D, C, F, B, A
- K · Potassium ion · metal · 11 copies · chains E, D, C, B, F, A
- MG · Magnesium ion · metal · 9 copies · chains E, D, C, B, F, A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 159 | 0.83 | 0.98 | 24 | empty |
| 2 | 700 | 0.74 | 0.80 | 49 | MG, ATP, K |
| 3 | 713 | 0.72 | 0.78 | 43 | MG, ATP, K |
| 4 | 698 | 0.72 | 0.79 | 41 | MG, ATP, K |
| 5 | 617 | 0.72 | 0.79 | 42 | MG, K, ATP |
Interfaces
7 interfaces between chains.
- C–B · 1601 Ų buried · 24 hydrogen bonds · protein-protein
- F–B · 1600 Ų buried · 29 hydrogen bonds · protein-protein
- C–F · 1581 Ų buried · 26 hydrogen bonds · protein-protein
- E–D · 1547 Ų buried · 29 hydrogen bonds · protein-protein
- E–B · 151 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 7RUT · Structure of Human ATP:Cobalamin Adenosyltransferase R190C bound to ATP · the same entry in another collection · chain D against D, TM-score 1.00
- Q96EY8 · AlphaFold monomer V2.0 prediction for corrinoid adenosyltransferase (Q96EY8) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 Q96EY8
- Elsewhere: RCSB PDB 7RUT · PDBe 7RUT · UniProt Q96EY8
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