MolNFT v1 · #67807 · protein
Crystal structure of pantothenate synthetase in complex with 2-(2- ((benzofuran-2-YLMETHOXY)CARBONYL)-5-methoxy-1H-indol-1-YL)ACETIC acid
3IVC: “Crystal structure of pantothenate synthetase in complex with 2-(2…”. X-ray diffraction, 2 ligands (FG4, SO4), 5 pockets (best druggability 0.84). MolNFT v1 #67807 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3IVC
- Type
- protein
- Length
- 575 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pantothenate synthetase
- EC
- 6.3.2.1
- UniProt
- P0A5R0
- Ligands
- FG4, SO4
- Pockets
- 5 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pantothenate synthetase (EC 6.3.2.1) | protein | 298 | 39% helix, 21% strand | P0A5R0 |
| B | Pantothenate synthetase (EC 6.3.2.1) | protein | 277 | 42% helix, 24% strand | P0A5R0 |
Ligands and binding sites
- FG4 · {2-[(1-benzofuran-2-ylmethoxy)carbonyl]-5-methoxy-1H-indol-1-yl}acetic acid · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A
- GOL · Glycerol · additive · 9 copies · chains A, B
- EOH · Ethanol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 443 | 0.84 | 0.91 | 64 | FG4 |
| 2 | 407 | 0.81 | 0.89 | 56 | FG4 |
| 3 | 422 | 0.68 | 0.80 | 30 | GOL, EOH |
| 4 | 66 | 0.31 | 0.75 | 25 | SO4 |
| 5 | 57 | 0.29 | 0.74 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1215 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 3IVC · Crystal structure of pantothenate synthetase in complex with… · the same entry in another collection · chain B against B, TM-score 1.00
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 P0A5R0
- Elsewhere: RCSB PDB 3IVC · PDBe 3IVC · UniProt P0A5R0
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