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Structure of ATP:CO(I)RRINOID adenosyltransferase (coba) from salmonella enterica in complex with four and five-coordinate COB(II) alamin and ATP
Analyse Structure of ATP:CO(I)RRINOID adenosyltransferase (coba) from salmonella… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HUT
- Type
- protein
- Length
- 360 residues
- Chains
- 2
- 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
- P31570
- Ligands
- ATP, B12, MG
- Pockets
- 2 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | COB(I)YRINIC acid A,C-diamide adenosyltransferase (EC 2.5.1.17) | protein | 191 | 43% helix, 18% strand | P31570 |
| B | COB(I)YRINIC acid A,C-diamide adenosyltransferase (EC 2.5.1.17) | protein | 169 | 42% helix, 20% strand | P31570 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
- B12 · Cobalamin · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 784 | 0.76 | 0.80 | 45 | MG, ATP, B12 |
| 2 | 367 | 0.61 | 0.77 | 40 | MG, ATP |
Interfaces
1 interface between chains.
- A–B · 2823 Ų buried · 56 hydrogen bonds · protein-protein
Compared structures
- 4HUT · Structure of ATP:co(I)rrinoid adenosyltransferase (CobA) from Salmonella enterica in… · the same entry in another collection · chain A against A, TM-score 1.00
- P31570 · AlphaFold monomer V2.0 prediction for corrinoid adenosyltransferase (P31570) · 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 P31570
- Elsewhere: RCSB PDB 4HUT · PDBe 4HUT · UniProt P31570
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