MolNFT v1 · #165036 · protein
Crystal structure of mycobacterium smegmatis coab in complex with CTP and (4-HYDROXYPHENYL)(2,3,4-TRIHYDROXYPHENYL)METHANONE
6THC · Coenzyme a biosynthesis bifunctional protein coabc: “Crystal structure of mycobacterium smegmatis coab in complex with CTP and…”. X-ray diffraction, 3 ligands (N9N, CTP, CA), 7 pockets (best druggability 0.80). MolNFT v1 #165036 on…
- PDB
- 6THC
- Type
- protein
- Length
- 874 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
- N9N, CTP, CA
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 28% 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 | 31% helix, 31% strand | A0QWT2 |
| B | Coenzyme a biosynthesis bifunctional protein coabc (EC 4.1.1.36, 6.3.2.5) | protein | 223 | 29% helix, 24% strand | A0QWT2 |
| C | Coenzyme a biosynthesis bifunctional protein coabc (EC 4.1.1.36, 6.3.2.5) | protein | 213 | 31% helix, 31% strand | A0QWT2 |
| D | Coenzyme a biosynthesis bifunctional protein coabc (EC 4.1.1.36, 6.3.2.5) | protein | 224 | 29% helix, 25% strand | A0QWT2 |
Ligands and binding sites
- N9N · (4-hydroxyphenyl)-[2,3,4-tris(oxidanyl)phenyl]methanone · ligand · 6 copies · chains A, B, C, D
- 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 · 3 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 831 | 0.80 | 0.83 | 84 | CTP, CA, N9N, ACT |
| 2 | 817 | 0.77 | 0.81 | 69 | CTP, CA, N9N |
| 3 | 840 | 0.76 | 0.80 | 80 | ACT, CTP, CA, N9N |
| 4 | 708 | 0.76 | 0.81 | 65 | CTP, CA, N9N, ACT |
| 5 | 414 | 0.68 | 0.81 | 36 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1225 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1129 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 373 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 345 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 321 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6THC · Crystal structure of Mycobacterium smegmatis CoaB in complex with CTP and… · 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 A 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 6THC · PDBe 6THC · UniProt A0QWT2
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