MolNFT v1 · #165021 · protein
Crystal structure of mycobacterium smegmatis coabc in complex with CTP and FMN
6TGV · Coenzyme a biosynthesis bifunctional protein coabc: “Crystal structure of mycobacterium smegmatis coabc in complex with CTP and FMN”. X-ray diffraction, 3 ligands (CTP, FMN, MG), 20 pockets (best druggability 0.74). MolNFT v1…
- PDB
- 6TGV
- Type
- protein
- Length
- 1,516 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, FMN, MG
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 23% 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 | 381 | 36% helix, 23% strand | A0QWT2 |
| B | Coenzyme a biosynthesis bifunctional protein coabc (EC 4.1.1.36, 6.3.2.5) | protein | 372 | 40% helix, 22% strand | A0QWT2 |
| C | Coenzyme a biosynthesis bifunctional protein coabc (EC 4.1.1.36, 6.3.2.5) | protein | 389 | 37% helix, 23% strand | A0QWT2 |
| D | Coenzyme a biosynthesis bifunctional protein coabc (EC 4.1.1.36, 6.3.2.5) | protein | 374 | 36% helix, 22% strand | A0QWT2 |
Ligands and binding sites
- CTP · Cytidine-5'-triphosphate · ligand · 4 copies · chains A, B, C, D
- FMN · Flavin mononucleotide · ligand · 4 copies · chains A, B, D, C
- MG · Magnesium ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1159 | 0.74 | 0.77 | 149 | CTP |
| 2 | 506 | 0.71 | 0.81 | 55 | EDO, FMN |
| 3 | 737 | 0.69 | 0.76 | 81 | EDO |
| 4 | 347 | 0.60 | 0.77 | 51 | CTP |
| 5 | 342 | 0.60 | 0.77 | 40 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1277 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1213 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 755 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 190 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6TGV · Crystal structure of Mycobacterium smegmatis CoaBC in complex with CTP and FMN · 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 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 A0QWT2
- Elsewhere: RCSB PDB 6TGV · PDBe 6TGV · UniProt A0QWT2
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