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Crystal structure of 2-dehydro-3-deoxyphosphogluconate aldolase from vibrio fischeri ES114
Analyse Crystal structure of 2-dehydro-3-deoxyphosphogluconate aldolase from vibrio… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NZR
- Type
- protein
- Length
- 980 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-dehydro-3-deoxyphosphogluconate aldolase
- EC
- 4.1.2.14, 4.1.3.16
- UniProt
- Q5E1U2
- Ligands
- MG
- Pockets
- 8 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | 2-dehydro-3-deoxyphosphogluconate aldolase (EC 4.1.2.14, 4.1.3.16) | protein | 245 | 43% helix, 19% strand | Q5E1U2 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 872 | 0.74 | 0.78 | 92 | empty |
| 2 | 831 | 0.73 | 0.78 | 79 | empty |
| 3 | 115 | 0.50 | 0.80 | 32 | empty |
| 4 | 134 | 0.49 | 0.79 | 34 | empty |
| 5 | 76 | 0.37 | 0.77 | 20 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1000 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 996 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 233 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 200 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 178 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 36 modified (engineered).
Compared structures
- 3NZR · Crystal structure of 2-dehydro-3-deoxyphosphogluconate aldolase from Vibrio fischeri ES114 · 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 Q5E1U2
- Elsewhere: RCSB PDB 3NZR · PDBe 3NZR · UniProt Q5E1U2
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