MolNFT v1 · #64165 · protein
Crystal structure of a member of enolase superfamily from roseovarius nubinhibens ism complexed with magnesium
3FVD · Mandelate RACEMASE/MUCONATE lactonizing enzyme: “Crystal structure of a member of enolase superfamily from roseovarius nubinhibens ism complexed with magnesium”. X-ray diffraction, 1 ligand (MG), 6 pockets (best druggability 0.78).…
- PDB
- 3FVD
- Type
- protein
- Length
- 728 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mandelate RACEMASE/MUCONATE lactonizing enzyme
- UniProt
- A3SNF7
- Ligands
- MG
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Mandelate RACEMASE/MUCONATE lactonizing enzyme | protein | 367 | 39% helix, 22% strand | A3SNF7 |
| A | Mandelate RACEMASE/MUCONATE lactonizing enzyme | protein | 361 | 40% helix, 19% strand | A3SNF7 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains B, A
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 | 1024 | 0.78 | 0.80 | 84 | empty |
| 2 | 518 | 0.71 | 0.80 | 65 | empty |
| 3 | 350 | 0.61 | 0.78 | 42 | MG |
| 4 | 69 | 0.33 | 0.76 | 20 | empty |
| 5 | 75 | 0.33 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- B–A · 764 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3FVD · Crystal structure of a member of enolase superfamily from ROSEOVARIUS NUBINHIBENS ISM… · 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 A3SNF7
- Elsewhere: RCSB PDB 3FVD · PDBe 3FVD · UniProt A3SNF7
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