MolNFT v1 · #99692 · protein
Crystal structure of TON1374
4MB0 · Phosphopantothenate synthetase: “Crystal structure of TON1374”. X-ray diffraction, 8 pockets (best druggability 0.84). MolNFT v1 #99692 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4MB0
- Type
- protein
- Length
- 1,015 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
- Pockets
- 8 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 54% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Phosphopantothenate synthetase (EC 6.3.2.26) | protein | 253 | 55% helix, 9% strand | B6YXQ1 |
| B | Phosphopantothenate synthetase (EC 6.3.2.26) | protein | 257 | 53% helix, 10% strand | B6YXQ1 |
| D | Phosphopantothenate synthetase (EC 6.3.2.26) | protein | 252 | 54% helix, 11% strand | B6YXQ1 |
Ligands and binding sites
- ACT · Acetate ion · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1132 | 0.84 | 0.85 | 106 | ACT |
| 2 | 1110 | 0.81 | 0.82 | 111 | empty |
| 3 | 436 | 0.80 | 0.88 | 59 | empty |
| 4 | 326 | 0.66 | 0.81 | 42 | empty |
| 5 | 85 | 0.42 | 0.79 | 14 | empty |
Interfaces
5 interfaces between chains.
- C–D · 2132 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 2118 Ų buried · 24 hydrogen bonds · protein-protein
- A–D · 369 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 225 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 93 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 4MB0 · PDBe 4MB0 · UniProt B6YXQ1
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