MolNFT v1 · #50291 · protein
Crystal structure of mandelate RACEMASE/MUCONATE lactonizing enzyme from roseovarius nubinhibens ism
2RDX · Mandelate RACEMASE/MUCONATE lactonizing enzyme, putative: “Crystal structure of mandelate RACEMASE/MUCONATE lactonizing enzyme from roseovarius nubinhibens ism”. X-ray diffraction, 1 ligand (MG), 20 pockets (best druggability 0.86).…
- PDB
- 2RDX
- Type
- protein
- Length
- 2,943 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mandelate RACEMASE/MUCONATE lactonizing enzyme, putative
- UniProt
- A3SNF8
- Ligands
- MG
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, F, H | Mandelate RACEMASE/MUCONATE lactonizing enzyme, putative | protein | 369 | 36% helix, 24% strand | A3SNF8 |
| E | Mandelate RACEMASE/MUCONATE lactonizing enzyme, putative | protein | 369 | 36% helix, 24% strand | A3SNF8 |
| G | Mandelate RACEMASE/MUCONATE lactonizing enzyme, putative | protein | 360 | 38% helix, 23% strand | A3SNF8 |
Ligands and binding sites
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- GOL · Glycerol · additive · 7 copies · chains A, C, D, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1059 | 0.86 | 0.87 | 139 | empty |
| 2 | 807 | 0.85 | 0.88 | 105 | empty |
| 3 | 513 | 0.81 | 0.87 | 69 | GOL |
| 4 | 679 | 0.80 | 0.85 | 80 | empty |
| 5 | 412 | 0.78 | 0.87 | 65 | empty |
Interfaces
16 interfaces between chains.
- E–G · 1274 Ų buried · 25 hydrogen bonds · protein-protein
- B–F · 1267 Ų buried · 23 hydrogen bonds · protein-protein
- D–H · 1266 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 1244 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 1080 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 2RDX · Crystal structure of mandelate racemase/muconate lactonizing enzyme from Roseovarius… · 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 A3SNF8
- Elsewhere: RCSB PDB 2RDX · PDBe 2RDX · UniProt A3SNF8
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