MolNFT v1 · #146047 · protein
Structure of human ATP:COBALAMIN adenosyltransferase bound to ATP, adenosylcobalamin, and triphosphate
6D5X · COB(I)YRINIC acid A,C-diamide adenosyltransferase…: “Structure of human ATP:COBALAMIN adenosyltransferase bound to ATP, adenosylcobalamin, and triphosphate”. X-ray diffraction, 6 ligands (5AD, B12, 3PO), 12 pockets (best…
- PDB
- 6D5X
- Type
- protein
- Length
- 515 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- COB(I)YRINIC acid A,C-diamide adenosyltransferase, mitochondrial
- EC
- 2.5.1.17
- UniProt
- Q96EY8
- Ligands
- 5AD, B12, 3PO, ATP, MG, SO4
- Pockets
- 12 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 64% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | COB(I)YRINIC acid A,C-diamide adenosyltransferase, mitochondrial (EC 2.5.1.17) | protein | 151 | 69% helix, 0% strand | Q96EY8 |
| B | COB(I)YRINIC acid A,C-diamide adenosyltransferase, mitochondrial (EC 2.5.1.17) | protein | 183 | 60% helix, 3% strand | Q96EY8 |
| C | COB(I)YRINIC acid A,C-diamide adenosyltransferase, mitochondrial (EC 2.5.1.17) | protein | 181 | 64% helix, 4% strand | Q96EY8 |
Ligands and binding sites
- 5AD · 5'-deoxyadenosine · ligand · 2 copies · chains A, C, B
- B12 · Cobalamin · ligand · 2 copies · chains A, C, B
- 3PO · Triphosphate · ligand · chains A, C
- ATP · Adenosine-5'-triphosphate · ligand · chains B, C
- MG · Magnesium ion · metal · 3 copies · chains A, C, B
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 150 | 0.83 | 0.98 | 26 | empty |
| 2 | 505 | 0.70 | 0.80 | 43 | 5AD, B12, MG, 3PO |
| 3 | 556 | 0.69 | 0.79 | 51 | ATP, MG |
| 4 | 272 | 0.58 | 0.78 | 29 | 5AD |
| 5 | 281 | 0.52 | 0.74 | 27 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1590 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1310 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 960 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6D5X · Structure of Human ATP:Cobalamin Adenosyltransferase bound to ATP, Adenosylcobalamin, and… · 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 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 6D5X · PDBe 6D5X · UniProt Q96EY8
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