Research workbench
Crystal structures of the wild-type, mutant-P1A and inactivated malonate semialdehyde decarboxylase: a structural basis for the decarboxylase and hydratase activities
Analyse Crystal structures of the wild-type, mutant-P1A and inactivated malonate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2AAL
- Type
- protein
- Length
- 775 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Malonate semialdehyde decarboxylase
- EC
- 4.1.1.-
- Pockets
- 3 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, E, F | Malonate semialdehyde decarboxylase (EC 4.1.1.-) | protein | 129 | 37% helix, 27% strand | — |
| B | Malonate semialdehyde decarboxylase (EC 4.1.1.-) | protein | 130 | 37% helix, 25% strand | — |
Ligands and binding sites
- MLI · Malonate ion · additive · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 204 | 0.82 | 0.97 | 28 | empty |
| 2 | 271 | 0.80 | 0.93 | 45 | empty |
| 3 | 112 | 0.61 | 0.87 | 21 | empty |
Interfaces
6 interfaces between chains.
- D–F · 1432 Ų buried · 31 hydrogen bonds · protein-protein
- E–F · 1417 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 1412 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 1411 Ų buried · 31 hydrogen bonds · protein-protein
- D–E · 1403 Ų buried · 31 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent (additive adduct).
Compared structures
- 2AAL · Crystal Structures of the Wild-type, Mutant-P1A and Inactivated Malonate Semialdehyde… · 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 2AAL · PDBe 2AAL
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