Research workbench
Cryo-EM structure of the S. typhimurium oxaloacetate decarboxylase beta-gamma sub-complex
Analyse Cryo-EM structure of the S. typhimurium oxaloacetate decarboxylase beta-gamma… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6IWW
- Type
- protein
- Length
- 1,386 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oxaloacetate decarboxylase beta chain; Probable oxaloacetate decarboxylase gamma chain
- EC
- 7.2.4.2
- UniProt
- A0A0F7JAV8, A0A0F7JC72
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 2 distinct chains · 72% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Oxaloacetate decarboxylase beta chain (EC 7.2.4.2) | protein | 420 | 70% helix, 0% strand | A0A0F7JAV8 |
| B, D, F | Probable oxaloacetate decarboxylase gamma chain (EC 7.2.4.2) | protein | 42 | 95% helix, 0% strand | A0A0F7JC72 |
Ligands and binding sites
- LMT · Dodecyl-beta-D-maltoside · additive · 3 copies · chains A, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 731 | 0.83 | 0.86 | 40 | LMT |
| 2 | 497 | 0.73 | 0.82 | 61 | empty |
| 3 | 656 | 0.72 | 0.79 | 62 | empty |
| 4 | 248 | 0.67 | 0.83 | 30 | empty |
| 5 | 293 | 0.67 | 0.82 | 34 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1600 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 1580 Ų buried · 1 hydrogen bond · protein-protein
- E–F · 1578 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 1539 Ų buried · 4 hydrogen bonds · protein-protein
- C–E · 1538 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6IWW · Cryo-EM structure of the S. typhimurium oxaloacetate decarboxylase beta-gamma sub-complex · 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 A0A0F7JAV8
- Every structure of UniProt A0A0F7JC72
- Elsewhere: RCSB PDB 6IWW · PDBe 6IWW · UniProt A0A0F7JAV8 · UniProt A0A0F7JC72
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