Research workbench
Crystal structure of the mutant E234A of galacturonate dehydratase from geobacillus sp. complexed with mg
Analyse Crystal structure of the mutant E234A of galacturonate dehydratase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3V5C
- Type
- protein
- Length
- 1,523 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mandelate RACEMASE/MUCONATE lactonizing protein
- UniProt
- D3EID5
- Ligands
- MG
- Pockets
- 9 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mandelate RACEMASE/MUCONATE lactonizing protein | protein | 386 | 35% helix, 25% strand | D3EID5 |
| B, D | Mandelate RACEMASE/MUCONATE lactonizing protein | protein | 376 | 35% helix, 26% strand | D3EID5 |
| C | Mandelate RACEMASE/MUCONATE lactonizing protein | protein | 385 | 35% helix, 26% strand | D3EID5 |
Ligands and binding sites
- MG · Magnesium ion · metal · 7 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 851 | 0.76 | 0.80 | 115 | MG |
| 2 | 846 | 0.75 | 0.79 | 121 | MG |
| 3 | 507 | 0.65 | 0.77 | 49 | empty |
| 4 | 76 | 0.50 | 0.84 | 27 | empty |
| 5 | 81 | 0.48 | 0.83 | 22 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1012 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1010 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 324 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 76 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 13 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3V5C · Crystal structure of the mutant E234A of Galacturonate Dehydratase from GEOBACILLUS SP.… · 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 D3EID5
- Elsewhere: RCSB PDB 3V5C · PDBe 3V5C · UniProt D3EID5
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