Research workbench
Crystal structure of TON1374 in complex with ATP
Analyse Crystal structure of TON1374 in complex with ATP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MB2
- Type
- protein
- Length
- 1,009 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphopantothenate synthetase
- EC
- 6.3.2.26
- UniProt
- B6YXQ1
- Ligands
- ATP, MG
- Pockets
- 7 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 55% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphopantothenate synthetase (EC 6.3.2.26) | protein | 252 | 57% helix, 10% strand | B6YXQ1 |
| B | Phosphopantothenate synthetase (EC 6.3.2.26) | protein | 257 | 53% helix, 9% strand | B6YXQ1 |
| C | Phosphopantothenate synthetase (EC 6.3.2.26) | protein | 246 | 56% helix, 11% strand | B6YXQ1 |
| D | Phosphopantothenate synthetase (EC 6.3.2.26) | protein | 254 | 55% helix, 10% strand | B6YXQ1 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · chains A
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 | 735 | 0.85 | 0.88 | 90 | ATP, MG |
| 2 | 678 | 0.79 | 0.83 | 69 | ATP |
| 3 | 473 | 0.72 | 0.82 | 52 | ATP |
| 4 | 244 | 0.67 | 0.84 | 31 | empty |
| 5 | 151 | 0.58 | 0.83 | 28 | empty |
Interfaces
5 interfaces between chains.
- C–D · 2141 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 2104 Ų buried · 27 hydrogen bonds · protein-protein
- A–D · 320 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 215 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 24 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
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 B6YXQ1
- Elsewhere: RCSB PDB 4MB2 · PDBe 4MB2 · UniProt B6YXQ1
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