Research workbench
Crystal structure of class II pyruvate aldolase from pseudomonas aeruginosa.
Analyse Crystal structure of class II pyruvate aldolase from pseudomonas aeruginosa. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7V8T
- Type
- protein
- Length
- 1,518 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase
- EC
- 4.1.2.52
- UniProt
- A0A081HJP9
- Ligands
- IOD
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase (EC 4.1.2.52) | protein | 253 | 47% helix, 17% strand | A0A081HJP9 |
Ligands and binding sites
- IOD · Iodide ion · ion · 10 copies · chains A, B, F, C, D, E
- P6G · Hexaethylene glycol · additive · 2 copies · chains A, D, B, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 608 | 0.84 | 0.89 | 48 | empty |
| 2 | 609 | 0.84 | 0.89 | 47 | empty |
| 3 | 1140 | 0.83 | 0.84 | 76 | empty |
| 4 | 860 | 0.77 | 0.80 | 104 | IOD |
| 5 | 445 | 0.68 | 0.80 | 56 | IOD |
Interfaces
12 interfaces between chains.
- B–C · 1630 Ų buried · 17 hydrogen bonds · protein-protein
- A–E · 1620 Ų buried · 13 hydrogen bonds · protein-protein
- D–F · 1608 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1065 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 1060 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7V8T · Crystal structure of class II pyruvate aldolase from Pseudomonas aeruginosa. · 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 A0A081HJP9
- Elsewhere: RCSB PDB 7V8T · PDBe 7V8T · UniProt A0A081HJP9
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