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Crystal structure of apo-LPG0406, a carboxymuconolactone decarboxylase family protein from legionella pneumophila
Analyse Crystal structure of apo-LPG0406, a carboxymuconolactone decarboxylase family… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DIK
- Type
- protein
- Length
- 336 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alkyl hydroperoxide reductase ahpd
- EC
- 1.11.1.15
- UniProt
- A0A0C9P2U2
- Pockets
- 3 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 83% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Alkyl hydroperoxide reductase ahpd (EC 1.11.1.15) | protein | 112 | 83% helix, 0% strand | A0A0C9P2U2 |
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 591 | 0.62 | 0.74 | 58 | empty |
| 2 | 62 | 0.40 | 0.80 | 15 | empty |
| 3 | 121 | 0.38 | 0.73 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1373 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 781 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 415 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 5DIK · Crystal structure of apo-lpg0406, a carboxymuconolactone decarboxylase family protein… · 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 A0A0C9P2U2
- Elsewhere: RCSB PDB 5DIK · PDBe 5DIK · UniProt A0A0C9P2U2
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