MolNFT v1 · #96533 · protein
Enduracididine biosynthesis enzyme mppr complexed with the condensation product of pyruvate and imidazole 4-carboxaldehyde
4JMD · Putative uncharacterized protein mppr: “Enduracididine biosynthesis enzyme mppr complexed with the condensation product of pyruvate and imidazole…”. X-ray diffraction, 1 ligand (4IC), 7 pockets (best druggability 0.77). MolNFT v1…
- PDB
- 4JMD
- Type
- protein
- Length
- 519 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative uncharacterized protein mppr
- UniProt
- Q643B8
- Ligands
- 4IC
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 12% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative uncharacterized protein mppr | protein | 257 | 12% helix, 51% strand | Q643B8 |
| B | Putative uncharacterized protein mppr | protein | 262 | 11% helix, 50% strand | Q643B8 |
Ligands and binding sites
- 4IC · (3E)-4-(1H-imidazol-4-yl)but-3-enoic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 172 | 0.77 | 0.93 | 27 | 4IC |
| 2 | 673 | 0.76 | 0.81 | 70 | empty |
| 3 | 140 | 0.74 | 0.92 | 27 | 4IC |
| 4 | 51 | 0.35 | 0.79 | 14 | empty |
| 5 | 69 | 0.33 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1528 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 4JMD · Enduracididine biosynthesis enzyme MppR complexed with the condensation product of… · the same entry in another collection · chain A against A, 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 Q643B8
- Elsewhere: RCSB PDB 4JMD · PDBe 4JMD · UniProt Q643B8
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