MolNFT v1 · #104735 · protein
Crystal structure of the C-terminal CTP-binding domain of a phosphopantothenoylcysteine DECARBOXYLASE/PHOSPHOPANTOTHENATE- cysteine ligase with bound CTP from mycobacterium smegmatis
4QJI · Phosphopantothenate--cysteine ligase: “Crystal structure of the C-terminal CTP-binding domain of a phosphopantothenoylcysteine…”. X-ray diffraction, 2 ligands (CTP, MG), 4 pockets (best druggability 0.67). MolNFT v1 #104735 on…
- PDB
- 4QJI
- Type
- protein
- Length
- 428 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphopantothenate--cysteine ligase
- EC
- 6.3.2.5
- UniProt
- A0QWT2
- Ligands
- CTP, MG
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphopantothenate--cysteine ligase (EC 6.3.2.5) | protein | 212 | 31% helix, 24% strand | A0QWT2 |
| B | Phosphopantothenate--cysteine ligase (EC 6.3.2.5) | protein | 216 | 31% helix, 25% strand | A0QWT2 |
Ligands and binding sites
- CTP · Cytidine-5'-triphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 614 | 0.67 | 0.76 | 63 | CTP, MG |
| 2 | 230 | 0.53 | 0.76 | 31 | CTP |
| 3 | 258 | 0.50 | 0.75 | 36 | empty |
| 4 | 57 | 0.33 | 0.77 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 717 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4QJI · Crystal Structure of the C-terminal CTP-binding domain of a Phosphopantothenoylcysteine… · the same entry in another collection · chain A against A, 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 4QJI · PDBe 4QJI · UniProt A0QWT2
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