Research workbench
Inferred ancestral pyruvate decarboxylase
Analyse Inferred ancestral pyruvate decarboxylase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NPU
- Type
- protein
- Length
- 2,182 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ANC27
- Ligands
- TPP, MG
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ANC27 | protein | 547 | 41% helix, 18% strand | — |
| B | ANC27 | protein | 545 | 40% helix, 17% strand | — |
| C | ANC27 | protein | 547 | 39% helix, 17% strand | — |
| D | ANC27 | protein | 543 | 40% helix, 17% strand | — |
Ligands and binding sites
- TPP · Thiamine diphosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 739 | 0.76 | 0.81 | 76 | empty |
| 2 | 796 | 0.76 | 0.80 | 71 | PEG |
| 3 | 627 | 0.73 | 0.80 | 56 | empty |
| 4 | 300 | 0.72 | 0.85 | 66 | MG, TPP |
| 5 | 213 | 0.69 | 0.86 | 46 | empty |
Interfaces
5 interfaces between chains.
- B–D · 1171 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 1053 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 286 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 264 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 153 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5NPU · Inferred ancestral pyruvate decarboxylase · 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
- Elsewhere: RCSB PDB 5NPU · PDBe 5NPU
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