Research workbench
Crystal structure of kdpg aldolase from legionella pneumophila with pyruvate captured at low pH as a covalent carbinolamine intermediate
Analyse Crystal structure of kdpg aldolase from legionella pneumophila with pyruvate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OVI
- Type
- protein
- Length
- 625 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Keto-deoxy-phosphogluconate aldolase
- EC
- 4.1.2.14, 4.1.3.16
- UniProt
- A0A2S6FBD8
- Ligands
- PVO, SO4
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Keto-deoxy-phosphogluconate aldolase (EC 4.1.2.14, 4.1.3.16) | protein | 210 | 42% helix, 16% strand | A0A2S6FBD8 |
| B | Keto-deoxy-phosphogluconate aldolase (EC 4.1.2.14, 4.1.3.16) | protein | 206 | 43% helix, 17% strand | A0A2S6FBD8 |
| C | Keto-deoxy-phosphogluconate aldolase (EC 4.1.2.14, 4.1.3.16) | protein | 209 | 43% helix, 16% strand | A0A2S6FBD8 |
Ligands and binding sites
- PVO · 2,2-bis(oxidanyl)propanoic acid · ligand · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 227 | 0.73 | 0.88 | 31 | SO4 |
| 2 | 107 | 0.66 | 0.90 | 30 | SO4 |
| 3 | 114 | 0.43 | 0.77 | 23 | SO4 |
| 4 | 135 | 0.41 | 0.74 | 24 | SO4 |
| 5 | 101 | 0.39 | 0.76 | 23 | PVO, SO4 |
Interfaces
3 interfaces between chains.
- B–C · 595 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 584 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 582 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 6OVI · Crystal Structure of KDPG Aldolase from Legionella Pneumophila with pyruvate captured at… · 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 A0A2S6FBD8
- Elsewhere: RCSB PDB 6OVI · PDBe 6OVI · UniProt A0A2S6FBD8
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