Research workbench
Crystal structure of putative methylmalonate-semialdehyde dehydrogenase from sinorhizobium meliloti 1021 complexed with NAD, target 011934
Analyse Crystal structure of putative methylmalonate-semialdehyde dehydrogenase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4IYM
- Type
- protein
- Length
- 7,819 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methylmalonate-semialdehyde dehydrogenase
- EC
- 1.2.1.27
- UniProt
- Q92RW4
- Ligands
- NAD, MG
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 5 distinct chains · 40% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, F, G, J, K, N | Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) | protein | 488 | 40% helix, 24% strand | Q92RW4 |
| C | Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) | protein | 491 | 40% helix, 23% strand | Q92RW4 |
| E | Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) | protein | 490 | 41% helix, 23% strand | Q92RW4 |
| H, I, L, M, P | Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) | protein | 489 | 41% helix, 24% strand | Q92RW4 |
| O | Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) | protein | 489 | 40% helix, 24% strand | Q92RW4 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 16 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
- MG · Magnesium ion · metal · 6 copies · chains A, F, G, I, O
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1142 | 0.86 | 0.87 | 76 | empty |
| 2 | 1200 | 0.86 | 0.87 | 76 | empty |
| 3 | 1183 | 0.85 | 0.86 | 73 | empty |
| 4 | 1179 | 0.85 | 0.86 | 71 | empty |
| 5 | 141 | 0.81 | 0.98 | 30 | empty |
Interfaces
34 interfaces between chains.
- C–D · 2688 Ų buried · 36 hydrogen bonds · protein-protein
- E–F · 2674 Ų buried · 34 hydrogen bonds · protein-protein
- I–J · 2673 Ų buried · 35 hydrogen bonds · protein-protein
- O–P · 2670 Ų buried · 35 hydrogen bonds · protein-protein
- G–H · 2667 Ų buried · 36 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 291 modified (engineered).
Compared structures
- 4IYM · Crystal structure of putative methylmalonate-semialdehyde dehydrogenase from… · 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 Q92RW4
- Elsewhere: RCSB PDB 4IYM · PDBe 4IYM · UniProt Q92RW4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.