MolNFT v1 · #168453 · protein
Mycobacterium tuberculosis pduo-type ATP:COBALAMIN adenosyltransferase bound to COB(II)ALAMIN and pppi
6WH5 · Corrinoid adenosyltransferase: “Mycobacterium tuberculosis pduo-type ATP:COBALAMIN adenosyltransferase bound to COB(II)ALAMIN and pppi”. X-ray diffraction, 4 ligands (3PO, B12, K), 5 pockets (best druggability 0.83). MolNFT v1…
- PDB
- 6WH5
- Type
- protein
- Length
- 558 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Corrinoid adenosyltransferase
- EC
- 2.5.1.17
- UniProt
- A0A045JVI3
- Ligands
- 3PO, B12, K, MG
- Pockets
- 5 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 56% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Corrinoid adenosyltransferase (EC 2.5.1.17) | protein | 186 | 56% helix, 6% strand | A0A045JVI3 |
Ligands and binding sites
- 3PO · Triphosphate · ligand · 3 copies · chains A, B, C
- B12 · Cobalamin · ligand · 3 copies · chains A, B, C
- K · Potassium ion · metal · 3 copies · chains A, C, B
- MG · Magnesium ion · metal · 3 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 199 | 0.83 | 0.97 | 36 | empty |
| 2 | 649 | 0.76 | 0.82 | 46 | 3PO, K, MG, B12 |
| 3 | 611 | 0.75 | 0.82 | 44 | 3PO, B12, K, MG |
| 4 | 602 | 0.74 | 0.81 | 45 | K, MG, 3PO, B12 |
| 5 | 494 | 0.64 | 0.77 | 31 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1707 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 1700 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 1691 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 6WH5 · Mycobacterium tuberculosis pduO-type ATP:cobalamin adenosyltransferase bound to… · the same entry in another collection · chain A against A, TM-score 1.00
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 A0A045JVI3
- Elsewhere: RCSB PDB 6WH5 · PDBe 6WH5 · UniProt A0A045JVI3
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