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Crystal structure of the mutant S29G.P34A of D-glucarate dehydratase from escherichia COLI complexed with product 5-keto-4-deoxy-D- glucarate
Analyse Crystal structure of the mutant S29G.P34A of D-glucarate dehydratase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PWG
- Type
- protein
- Length
- 1,744 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucarate dehydratase
- UniProt
- E2KTD9
- Ligands
- GLR, MG
- Pockets
- 13 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glucarate dehydratase | protein | 442 | 40% helix, 17% strand | E2KTD9 |
| C | Glucarate dehydratase | protein | 433 | 39% helix, 18% strand | E2KTD9 |
| D | Glucarate dehydratase | protein | 427 | 39% helix, 19% strand | E2KTD9 |
Ligands and binding sites
- GLR · 2,3-dihydroxy-5-oxo-hexanedioate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 3 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, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 955 | 0.82 | 0.84 | 127 | GOL |
| 2 | 742 | 0.78 | 0.82 | 98 | empty |
| 3 | 276 | 0.71 | 0.86 | 53 | GOL |
| 4 | 694 | 0.71 | 0.78 | 70 | GLR |
| 5 | 302 | 0.68 | 0.83 | 40 | empty |
Interfaces
6 interfaces between chains.
- B–D · 1612 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 1610 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 690 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 678 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 352 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3PWG · Crystal structure of the mutant S29G.P34A of D-Glucarate dehydratase from Escherichia… · 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 E2KTD9
- Elsewhere: RCSB PDB 3PWG · PDBe 3PWG · UniProt E2KTD9
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