Research workbench
Crystal structure of pantothenate synthetase in complex with 2-(5- methoxy-2-(2-nitro-4-(TRIFLUOROMETHYL)PHENYLSULFONYLCARBAMOYL)-1H- indol-1-YL)ACETIC acid
Analyse Crystal structure of pantothenate synthetase in complex with 2-(5… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MUN
- Type
- protein
- Length
- 555 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
- 2DZ
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pantothenate synthetase (EC 6.3.2.1) | protein | 283 | 42% helix, 23% strand | P0A5R0 |
| B | Pantothenate synthetase (EC 6.3.2.1) | protein | 272 | 42% helix, 24% strand | P0A5R0 |
Ligands and binding sites
- 2DZ · [5-methoxy-2-({[2-nitro-4-(trifluoromethyl)phenyl]sulfonyl}carbamoyl)-1H-indol-1-yl]acetic acid · ligand · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B
- EOH · Ethanol · additive · 3 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 559 | 0.82 | 0.88 | 56 | 2DZ, GOL |
| 2 | 499 | 0.76 | 0.84 | 49 | 2DZ |
| 3 | 249 | 0.56 | 0.78 | 28 | GOL, EDO |
| 4 | 51 | 0.35 | 0.79 | 19 | EDO |
| 5 | 62 | 0.33 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1241 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 4MUN · 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 4MUN · PDBe 4MUN · UniProt P0A5R0
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