Research workbench
Crystal structure of methylmalonate semialdehyde dehydrogenase from bacillus subtilis
Analyse Crystal structure of methylmalonate semialdehyde dehydrogenase from bacillus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1T90
- Type
- protein
- Length
- 1,936 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable methylmalonate-semialdehyde dehydrogenase
- EC
- 1.2.1.27
- UniProt
- P42412
- Ligands
- NAD
- Pockets
- 18 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Probable methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) | protein | 484 | 40% helix, 24% strand | P42412 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1176 | 0.87 | 0.88 | 119 | empty |
| 2 | 158 | 0.83 | 0.99 | 27 | empty |
| 3 | 148 | 0.83 | 0.99 | 30 | empty |
| 4 | 531 | 0.70 | 0.79 | 62 | empty |
| 5 | 512 | 0.70 | 0.79 | 58 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2762 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 2757 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 1756 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 1718 Ų buried · 23 hydrogen bonds · protein-protein
- A–D · 1023 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 1T90 · Crystal structure of methylmalonate semialdehyde dehydrogenase from Bacillus subtilis · the same entry in another collection · chain A against A, TM-score 1.00
- P42412 · AlphaFold monomer V2.0 prediction for malonate-semialdehyde dehydrogenase (P42412) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P42412
- Elsewhere: RCSB PDB 1T90 · PDBe 1T90 · UniProt P42412
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