Research workbench
Crystal structure of D-glucarate dehydratase from ralstonia solanacearum complexed with mg and D-glucarate
Analyse Crystal structure of D-glucarate dehydratase from ralstonia solanacearum… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3P0W
- Type
- protein
- Length
- 1,698 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mandelate RACEMASE/MUCONATE lactonizing protein
- UniProt
- B2UIZ1
- Ligands
- GKR, MG
- Pockets
- 13 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mandelate RACEMASE/MUCONATE lactonizing protein | protein | 424 | 40% helix, 19% strand | B2UIZ1 |
| B | Mandelate RACEMASE/MUCONATE lactonizing protein | protein | 428 | 39% helix, 18% strand | B2UIZ1 |
| C | Mandelate RACEMASE/MUCONATE lactonizing protein | protein | 421 | 40% helix, 19% strand | B2UIZ1 |
| D | Mandelate RACEMASE/MUCONATE lactonizing protein | protein | 425 | 41% helix, 19% strand | B2UIZ1 |
Ligands and binding sites
- GKR · D-glucarate · ligand · 4 copies · chains A, B, C, D
- 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
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 676 | 0.80 | 0.85 | 72 | empty |
| 2 | 401 | 0.79 | 0.88 | 52 | empty |
| 3 | 1073 | 0.72 | 0.76 | 73 | empty |
| 4 | 542 | 0.71 | 0.80 | 65 | GKR |
| 5 | 474 | 0.67 | 0.79 | 54 | GKR |
Interfaces
4 interfaces between chains.
- A–B · 1447 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1416 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 166 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 36 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3P0W · Crystal structure of D-Glucarate dehydratase from Ralstonia solanacearum complexed with… · 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 B2UIZ1
- Elsewhere: RCSB PDB 3P0W · PDBe 3P0W · UniProt B2UIZ1
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