MolNFT v1 · #186922 · protein
Structure of human ATP:COBALAMIN adenosyltransferase E193K bound to adenosylcobalamin
7RUV · Corrinoid adenosyltransferase: “Structure of human ATP:COBALAMIN adenosyltransferase E193K bound to adenosylcobalamin”. X-ray diffraction, 4 ligands (B12, 5AD, MG), 5 pockets (best druggability 0.61). MolNFT v1 #186922 on GenesisL1…
- PDB
- 7RUV
- Type
- protein
- Length
- 599 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Corrinoid adenosyltransferase
- EC
- 2.5.1.17
- UniProt
- Q96EY8
- Ligands
- B12, 5AD, MG, K
- Pockets
- 5 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 71% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Corrinoid adenosyltransferase (EC 2.5.1.17) | protein | 150 | 71% helix, 0% strand | Q96EY8 |
| B | Corrinoid adenosyltransferase (EC 2.5.1.17) | protein | 147 | 71% helix, 0% strand | Q96EY8 |
| C, D | Corrinoid adenosyltransferase (EC 2.5.1.17) | protein | 151 | 72% helix, 0% strand | Q96EY8 |
Ligands and binding sites
- B12 · Cobalamin · ligand · 4 copies · chains A, D, B, C
- 5AD · 5'-deoxyadenosine · ligand · 4 copies · chains A, D, B, C
- MG · Magnesium ion · metal · 2 copies · chains A, C
- K · Potassium ion · metal · chains A
- GOL · Glycerol · additive · chains A, 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 335 | 0.61 | 0.78 | 36 | 5AD |
| 2 | 197 | 0.48 | 0.76 | 17 | empty |
| 3 | 91 | 0.42 | 0.78 | 15 | empty |
| 4 | 109 | 0.34 | 0.73 | 16 | empty |
| 5 | 51 | 0.26 | 0.73 | 14 | empty |
Interfaces
3 interfaces between chains.
- B–D · 992 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 50 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 22 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7RUV · Structure of Human ATP:Cobalamin Adenosyltransferase E193K bound to adenosylcobalamin · the same entry in another collection · chain A against A, TM-score 1.00
- Q96EY8 · AlphaFold monomer V2.0 prediction for corrinoid adenosyltransferase (Q96EY8) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 7RUV · PDBe 7RUV · UniProt Q96EY8
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