MolNFT v1 · #40043 · protein
Structure of human ATP:COBALAMIN adenosyltransferase bound to ATP.
2IDX · COB(I)YRINIC acid A,C-diamide adenosyltransferase: “Structure of human ATP:COBALAMIN adenosyltransferase bound to ATP.”. X-ray diffraction, 4 ligands (ATP, MG, SO4), 10 pockets (best druggability 0.81). MolNFT v1 #40043 on…
- PDB
- 2IDX
- Type
- protein
- Length
- 506 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- COB(I)YRINIC acid A,C-diamide adenosyltransferase
- EC
- 2.5.1.17
- UniProt
- Q96EY8
- Ligands
- ATP, MG, SO4, CL
- Pockets
- 10 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 62% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | COB(I)YRINIC acid A,C-diamide adenosyltransferase (EC 2.5.1.17) | protein | 148 | 68% helix, 1% strand | Q96EY8 |
| B | COB(I)YRINIC acid A,C-diamide adenosyltransferase (EC 2.5.1.17) | protein | 178 | 58% helix, 4% strand | Q96EY8 |
| C | COB(I)YRINIC acid A,C-diamide adenosyltransferase (EC 2.5.1.17) | protein | 180 | 62% helix, 4% strand | Q96EY8 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, C, B
- MG · Magnesium ion · metal · 4 copies · chains A, C, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, C
- CL · Chloride ion · ion · chains A, B, 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 127 | 0.81 | 0.98 | 24 | empty |
| 2 | 533 | 0.72 | 0.81 | 42 | MG, ATP |
| 3 | 384 | 0.66 | 0.79 | 41 | MG, ATP |
| 4 | 75 | 0.56 | 0.88 | 21 | empty |
| 5 | 297 | 0.51 | 0.74 | 32 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1562 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 1531 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 967 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 2IDX · Structure of Human ATP:Cobalamin adenosyltransferase bound to ATP. · 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 B 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 2IDX · PDBe 2IDX · UniProt Q96EY8
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