MolNFT v1 · #146034 · protein
Structure of human ATP:COBALAMIN adenosyltransferase bound to ATP, and adenosylcobalamin
6D5K · COB(I)YRINIC acid A,C-diamide adenosyltransferase…: “Structure of human ATP:COBALAMIN adenosyltransferase bound to ATP, and adenosylcobalamin”. X-ray diffraction, 5 ligands (5AD, B12, ATP), 10 pockets (best druggability 0.81).…
- PDB
- 6D5K
- Type
- protein
- Length
- 512 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, ATP, MG, SO4
- Pockets
- 10 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 64% helix, 4% 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 | 152 | 69% helix, 1% strand | Q96EY8 |
| B | COB(I)YRINIC acid A,C-diamide adenosyltransferase, mitochondrial (EC 2.5.1.17) | protein | 182 | 62% helix, 4% strand | Q96EY8 |
| C | COB(I)YRINIC acid A,C-diamide adenosyltransferase, mitochondrial (EC 2.5.1.17) | protein | 178 | 62% 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
- ATP · Adenosine-5'-triphosphate · ligand · chains B, C
- MG · Magnesium ion · metal · 2 copies · chains B, C
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, C
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 139 | 0.81 | 0.98 | 24 | empty |
| 2 | 553 | 0.70 | 0.79 | 43 | ATP, MG |
| 3 | 417 | 0.69 | 0.81 | 38 | 5AD, B12 |
| 4 | 247 | 0.57 | 0.78 | 27 | 5AD |
| 5 | 204 | 0.47 | 0.75 | 20 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1586 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 1235 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 980 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 6D5K · Structure of Human ATP:Cobalamin Adenosyltransferase bound to ATP, and 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 C 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 6D5K · PDBe 6D5K · UniProt Q96EY8
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