MolNFT v1 · #93618 · protein
Crystal structure of mandelate RACEMASE/MUCONATE lactonizing enzyme (efi TARGET:502127)
4H83: “Crystal structure of mandelate RACEMASE/MUCONATE lactonizing enzyme (efi TARGET:502127)”. X-ray diffraction, 3 ligands (BCT, NA, PO4), 16 pockets (best druggability 0.86). MolNFT v1 #93618 on GenesisL1: 3D structure, binding sites…
- PDB
- 4H83
- Type
- protein
- Length
- 2,155 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mandelate RACEMASE/MUCONATE lactonizing enzyme
- UniProt
- A4AFX2
- Ligands
- BCT, NA, PO4
- Pockets
- 16 · best druggability 0.86
Structure
x-ray diffraction · 6 distinct chains · 41% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mandelate RACEMASE/MUCONATE lactonizing enzyme | protein | 356 | 42% helix, 21% strand | A4AFX2 |
| B | Mandelate RACEMASE/MUCONATE lactonizing enzyme | protein | 354 | 42% helix, 20% strand | A4AFX2 |
| C | Mandelate RACEMASE/MUCONATE lactonizing enzyme | protein | 356 | 42% helix, 21% strand | A4AFX2 |
| D | Mandelate RACEMASE/MUCONATE lactonizing enzyme | protein | 366 | 41% helix, 21% strand | A4AFX2 |
| E | Mandelate RACEMASE/MUCONATE lactonizing enzyme | protein | 355 | 43% helix, 20% strand | A4AFX2 |
| F | Mandelate RACEMASE/MUCONATE lactonizing enzyme | protein | 368 | 40% helix, 23% strand | A4AFX2 |
Ligands and binding sites
- BCT · Bicarbonate ion · ligand · 2 copies · chains A, F
- NA · Sodium ion · metal · 8 copies · chains A, D, F, B, C, E
- PO4 · Phosphate ion · ion · chains C, F
- GOL · Glycerol · additive · chains C, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 349 | 0.86 | 0.95 | 39 | empty |
| 2 | 345 | 0.86 | 0.95 | 40 | empty |
| 3 | 1124 | 0.86 | 0.87 | 117 | empty |
| 4 | 1078 | 0.86 | 0.87 | 105 | PO4 |
| 5 | 325 | 0.85 | 0.95 | 43 | empty |
Interfaces
12 interfaces between chains.
- C–F · 1266 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1225 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1214 Ų buried · 17 hydrogen bonds · protein-protein
- E–F · 1212 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 1119 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 4H83 · Crystal structure of Mandelate racemase/muconate lactonizing enzyme (EFI target:502127) · 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 A4AFX2
- Elsewhere: RCSB PDB 4H83 · PDBe 4H83 · UniProt A4AFX2
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