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Crystal structure of D-mannonate dehydratase from novosphingobium aromaticivorans
Analyse Crystal structure of D-mannonate dehydratase from novosphingobium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2QJJ
- Type
- protein
- Length
- 1,575 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mandelate RACEMASE/MUCONATE lactonizing enzyme
- UniProt
- A4XF23
- Ligands
- MG
- Pockets
- 10 · best druggability 0.88
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Mandelate RACEMASE/MUCONATE lactonizing enzyme | protein | 402 | 38% helix, 19% strand | A4XF23 |
| C | Mandelate RACEMASE/MUCONATE lactonizing enzyme | protein | 384 | 40% helix, 20% strand | A4XF23 |
| D | Mandelate RACEMASE/MUCONATE lactonizing enzyme | protein | 387 | 40% helix, 19% strand | A4XF23 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 677 | 0.88 | 0.93 | 98 | empty |
| 2 | 102 | 0.77 | 0.98 | 35 | empty |
| 3 | 286 | 0.73 | 0.86 | 43 | empty |
| 4 | 58 | 0.69 | 0.97 | 27 | empty |
| 5 | 389 | 0.65 | 0.79 | 45 | empty |
Interfaces
5 interfaces between chains.
- C–D · 2688 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 2677 Ų buried · 34 hydrogen bonds · protein-protein
- A–D · 1375 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 1098 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 1082 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 2QJJ · Crystal structure of D-Mannonate dehydratase from Novosphingobium aromaticivorans · 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 D 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 2QJJ · PDBe 2QJJ · UniProt A4XF23
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