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Crystal structure of mtb aspartate decarboxylase, pyrazinoic acid complex
Analyse Crystal structure of mtb aspartate decarboxylase, pyrazinoic acid complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OYY
- Type
- protein
- Length
- 684 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aspartate 1-decarboxylase beta chain; Aspartate 1-decarboxylase alpha chain
- EC
- 4.1.1.11
- UniProt
- P9WIL3
- Ligands
- PYR, VGL
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 14% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, I, E, K, G | Aspartate 1-decarboxylase beta chain | protein | 24 | 0% helix, 67% strand | P9WIL3 |
| B, D, J, F, L, H | Aspartate 1-decarboxylase alpha chain (EC 4.1.1.11) | protein | 90 | 18% helix, 43% strand | P9WIL3 |
Ligands and binding sites
- PYR · Pyruvic acid · ligand · 6 copies · chains B, D, J, F, L, G, H
- VGL · Pyrazine-2-carboxylic acid · ligand · 6 copies · chains B, C, D, J, F, I, L, E, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 57 | 0.70 | 0.97 | 17 | PYR, VGL |
| 2 | 94 | 0.62 | 0.88 | 27 | PYR, VGL |
| 3 | 159 | 0.43 | 0.75 | 28 | empty |
| 4 | 158 | 0.41 | 0.74 | 26 | empty |
Interfaces
20 interfaces between chains.
- A–B · 1674 Ų buried · 37 hydrogen bonds · protein-protein
- I–J · 1671 Ų buried · 40 hydrogen bonds · protein-protein
- E–F · 1667 Ų buried · 41 hydrogen bonds · protein-protein
- C–D · 1652 Ų buried · 38 hydrogen bonds · protein-protein
- K–L · 1643 Ų buried · 38 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent (covalent ligand).
Compared structures
- 6OYY · Crystal structure of Mtb aspartate decarboxylase, pyrazinoic acid complex · the same entry in another collection · chain H against H, 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 P9WIL3
- Elsewhere: RCSB PDB 6OYY · PDBe 6OYY · UniProt P9WIL3
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