Research workbench
Crystal structure of a putative kdpg (2-keto-3-deoxy-6- phosphogluconate) aldolase from oleispira antarctica
Analyse Crystal structure of a putative kdpg (2-keto-3-deoxy-6- phosphogluconate)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VCR
- Type
- protein
- Length
- 432 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative kdpg (2-keto-3-deoxy-6-phosphogluconate) aldolase
- UniProt
- D2YW47
- Ligands
- PYR
- Pockets
- 4 · best druggability 0.53
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Putative kdpg (2-keto-3-deoxy-6-phosphogluconate) aldolase | protein | 216 | 45% helix, 18% strand | D2YW47 |
Ligands and binding sites
- PYR · Pyruvic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 174 | 0.53 | 0.78 | 20 | empty |
| 2 | 178 | 0.53 | 0.78 | 22 | empty |
| 3 | 138 | 0.42 | 0.75 | 22 | empty |
| 4 | 56 | 0.39 | 0.81 | 18 | PYR |
Interfaces
1 interface between chains.
- A–B · 217 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 3VCR · Crystal structure of a putative Kdpg (2-keto-3-deoxy-6-phosphogluconate) aldolase from… · 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 D2YW47
- Elsewhere: RCSB PDB 3VCR · PDBe 3VCR · UniProt D2YW47
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