MolNFT v1 · #97040 · protein
Crystal structure of the A314P mutant of mannonate dehydratase from novosphingobium aromaticivorans complexed with mg and D-mannonate
4K1W · Mandelate RACEMASE/MUCONATE lactonizing enzyme, N-terminal…: “Crystal structure of the A314P mutant of mannonate dehydratase from novosphingobium aromaticivorans complexed…”. X-ray diffraction, 4 ligands (CS2, MG, CO2), 15 pockets…
- PDB
- 4K1W
- Type
- protein
- Length
- 1,549 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mandelate RACEMASE/MUCONATE lactonizing enzyme, N-terminal domain protein
- UniProt
- A4XF23
- Ligands
- CS2, MG, CO2, CO3
- Pockets
- 15 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mandelate RACEMASE/MUCONATE lactonizing enzyme, N-terminal domain protein | protein | 395 | 39% helix, 20% strand | A4XF23 |
| B | Mandelate RACEMASE/MUCONATE lactonizing enzyme, N-terminal domain protein | protein | 386 | 40% helix, 20% strand | A4XF23 |
| C, D | Mandelate RACEMASE/MUCONATE lactonizing enzyme, N-terminal domain protein | protein | 384 | 40% helix, 20% strand | A4XF23 |
Ligands and binding sites
- CS2 · D-mannonic acid · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 5 copies · chains A, B, D, C
- CO2 · Carbon dioxide · ion · 5 copies · chains A, B, C, D
- CO3 · Carbonate ion · ion · chains C
- PGE · Triethylene glycol · additive · 4 copies · chains A, B, D, C
- PDO · 1,3-propandiol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 393 | 0.84 | 0.92 | 69 | empty |
| 2 | 157 | 0.79 | 0.95 | 29 | empty |
| 3 | 247 | 0.75 | 0.89 | 34 | empty |
| 4 | 61 | 0.70 | 0.97 | 28 | empty |
| 5 | 57 | 0.70 | 0.98 | 23 | empty |
Interfaces
5 interfaces between chains.
- C–D · 2704 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 2697 Ų buried · 35 hydrogen bonds · protein-protein
- A–D · 1515 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 1116 Ų buried · 21 hydrogen bonds · protein-protein
- B–D · 1106 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 4K1W · Crystal structure of the A314P mutant of mannonate dehydratase from novosphingobium… · the same entry in another collection · chain A against A, TM-score 1.00
- A4XF23 · AlphaFold monomer V2.0 prediction for D-mannonate dehydratase (A4XF23) · a predicted model of the same protein · chain B 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 A4XF23
- Elsewhere: RCSB PDB 4K1W · PDBe 4K1W · UniProt A4XF23
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