MolNFT v1 · #75234 · protein
Crystal structure of D-mannonate dehydratase from chromohalobacter salexigens with mg and glycerol bound in the active site
3PK7 · Mandelate RACEMASE/MUCONATE lactonizing enzyme: “Crystal structure of D-mannonate dehydratase from chromohalobacter salexigens with mg and glycerol bound in…”. X-ray diffraction, 1 ligand (MG), 20 pockets (best druggability 0.89).…
- PDB
- 3PK7
- Type
- protein
- Length
- 3,126 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mandelate RACEMASE/MUCONATE lactonizing enzyme
- UniProt
- Q1QT89
- Ligands
- MG
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 8 distinct chains · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mandelate RACEMASE/MUCONATE lactonizing enzyme | protein | 396 | 39% helix, 20% strand | Q1QT89 |
| B | Mandelate RACEMASE/MUCONATE lactonizing enzyme | protein | 384 | 40% helix, 20% strand | Q1QT89 |
| C | Mandelate RACEMASE/MUCONATE lactonizing enzyme | protein | 395 | 39% helix, 20% strand | Q1QT89 |
| D | Mandelate RACEMASE/MUCONATE lactonizing enzyme | protein | 387 | 40% helix, 20% strand | Q1QT89 |
| E | Mandelate RACEMASE/MUCONATE lactonizing enzyme | protein | 396 | 39% helix, 20% strand | Q1QT89 |
| F | Mandelate RACEMASE/MUCONATE lactonizing enzyme | protein | 386 | 40% helix, 20% strand | Q1QT89 |
| G | Mandelate RACEMASE/MUCONATE lactonizing enzyme | protein | 388 | 39% helix, 20% strand | Q1QT89 |
| H | Mandelate RACEMASE/MUCONATE lactonizing enzyme | protein | 394 | 39% helix, 20% strand | Q1QT89 |
Ligands and binding sites
- MG · Magnesium ion · metal · 9 copies · chains A, B, C, D, E, F, G, H
- GOL · Glycerol · additive · 8 copies · chains A, B, C, D, E, H, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 667 | 0.89 | 0.93 | 100 | empty |
| 2 | 646 | 0.88 | 0.93 | 97 | empty |
| 3 | 321 | 0.79 | 0.89 | 48 | empty |
| 4 | 112 | 0.77 | 0.97 | 42 | empty |
| 5 | 107 | 0.77 | 0.97 | 34 | empty |
Interfaces
14 interfaces between chains.
- F–G · 2753 Ų buried · 38 hydrogen bonds · protein-protein
- E–H · 2744 Ų buried · 42 hydrogen bonds · protein-protein
- A–B · 2737 Ų buried · 39 hydrogen bonds · protein-protein
- C–D · 2718 Ų buried · 34 hydrogen bonds · protein-protein
- B–F · 1369 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 3PK7 · Crystal structure of D-mannonate dehydratase from Chromohalobacter salexigens with MG and… · the same entry in another collection · chain H against H, TM-score 1.00
- Q1QT89 · AlphaFold monomer V2.0 prediction for D-galactonate dehydratase family member mand… · a predicted model of the same protein · 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 Q1QT89
- Elsewhere: RCSB PDB 3PK7 · PDBe 3PK7 · UniProt Q1QT89
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