Research workbench
Crystal structure of mycobacterium smegmatis coabc in complex with CTP and FMN
Analyse Crystal structure of mycobacterium smegmatis coabc in complex with CTP and FMN in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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