Research workbench
Structure of bacterial enzyme in complex with cofactor
Analyse Structure of bacterial enzyme in complex with cofactor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ITA
- Type
- protein
- Length
- 904 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Succinate-semialdehyde dehydrogenase
- UniProt
- B1XMM6
- Ligands
- NDP
- Pockets
- 8 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Succinate-semialdehyde dehydrogenase | protein | 452 | 45% helix, 20% strand | B1XMM6 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 34 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1105 | 0.83 | 0.84 | 119 | EDO |
| 2 | 339 | 0.61 | 0.78 | 45 | NDP, EDO |
| 3 | 362 | 0.60 | 0.77 | 51 | NDP, EDO |
| 4 | 232 | 0.57 | 0.78 | 30 | EDO |
| 5 | 248 | 0.55 | 0.77 | 30 | EDO |
Interfaces
1 interface between chains.
- A–B · 2429 Ų buried · 36 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 4ITA · Structure of bacterial enzyme in complex with cofactor · 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 B1XMM6
- Elsewhere: RCSB PDB 4ITA · PDBe 4ITA · UniProt B1XMM6
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