Research workbench
Structure of a putative pyruvate dehydrogenase from the photosynthetic bacterium rhodopseudomonas palustrus CGA009
Analyse Structure of a putative pyruvate dehydrogenase from the photosynthetic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IC3
- Type
- protein
- Length
- 376 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative pyruvate dehydrogenase
- UniProt
- Q6N5V5
- Ligands
- BGC, K, NA, PO4
- Pockets
- 1 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative pyruvate dehydrogenase | protein | 98 | 38% helix, 20% strand | Q6N5V5 |
| B | Putative pyruvate dehydrogenase | protein | 96 | 39% helix, 17% strand | Q6N5V5 |
| C | Putative pyruvate dehydrogenase | protein | 97 | 42% helix, 20% strand | Q6N5V5 |
| D | Putative pyruvate dehydrogenase | protein | 85 | 45% helix, 19% strand | Q6N5V5 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · chains A, B, C, D
- K · Potassium ion · metal · chains B, D
- NA · Sodium ion · metal · chains C
- PO4 · Phosphate ion · ion · 3 copies · chains B, C, D, A
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 902 | 0.75 | 0.78 | 86 | EDO, BGC, PO4 |
Interfaces
6 interfaces between chains.
- B–C · 3488 Ų buried · 42 hydrogen bonds · protein-protein
- A–D · 3358 Ų buried · 41 hydrogen bonds · protein-protein
- A–C · 634 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 374 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 307 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 3IC3 · Structure of a putative pyruvate dehydrogenase from the photosynthetic bacterium… · 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 Q6N5V5
- Elsewhere: RCSB PDB 3IC3 · PDBe 3IC3 · UniProt Q6N5V5
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