Research workbench
Crystal structure of mycobacterium smegmatis coab in complex with CTP
Analyse Crystal structure of mycobacterium smegmatis coab in complex with CTP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TH2
- Type
- protein
- Length
- 880 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coenzyme a biosynthesis bifunctional protein coabc
- EC
- 4.1.1.36, 6.3.2.5
- UniProt
- A0QWT2
- Ligands
- CTP, CA
- Pockets
- 13 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Coenzyme a biosynthesis bifunctional protein coabc (EC 4.1.1.36, 6.3.2.5) | protein | 214 | 29% helix, 29% strand | A0QWT2 |
| B, D | Coenzyme a biosynthesis bifunctional protein coabc (EC 4.1.1.36, 6.3.2.5) | protein | 229 | 29% helix, 24% strand | A0QWT2 |
| C | Coenzyme a biosynthesis bifunctional protein coabc (EC 4.1.1.36, 6.3.2.5) | protein | 208 | 32% helix, 29% strand | A0QWT2 |
Ligands and binding sites
- CTP · Cytidine-5'-triphosphate · ligand · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 5 copies · chains A, B, C, D
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 919 | 0.75 | 0.79 | 95 | CTP, CA, ACT, MES |
| 2 | 880 | 0.73 | 0.78 | 78 | CTP, CA, ACT, MES |
| 3 | 655 | 0.72 | 0.79 | 59 | CTP, CA, ACT, MES |
| 4 | 538 | 0.69 | 0.79 | 50 | CTP, CA, ACT, MES |
| 5 | 200 | 0.47 | 0.75 | 33 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1280 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1106 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 381 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 341 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 183 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6TH2 · Crystal structure of Mycobacterium smegmatis CoaB in complex with CTP · the same entry in another collection · chain D against D, TM-score 1.00
- A0QWT2 · AlphaFold monomer V2.0 prediction for coenzyme a biosynthesis bifunctional protein coabc… · 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 A0QWT2
- Elsewhere: RCSB PDB 6TH2 · PDBe 6TH2 · UniProt A0QWT2
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