Research workbench
Crystal structure of FG41MALONATE semialdehyde decarboxylase inhibited by 3-bromopropiolate
Analyse Crystal structure of FG41MALONATE semialdehyde decarboxylase inhibited by… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LHO
- Type
- protein
- Length
- 655 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- FG41 malonate semialdehyde decarboxylase
- EC
- 4.1.1.-
- UniProt
- F2Z288
- Ligands
- PR6, PO4
- Pockets
- 7 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | FG41 malonate semialdehyde decarboxylase (EC 4.1.1.-) | protein | 131 | 36% helix, 28% strand | F2Z288 |
Ligands and binding sites
- PR6 · 3-chloro-3-oxopropanoic acid · ligand · 5 copies · chains A, B, C, D, E
- PO4 · Phosphate ion · ion · 15 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 538 | 0.65 | 0.76 | 46 | empty |
| 2 | 470 | 0.64 | 0.77 | 45 | empty |
| 3 | 95 | 0.53 | 0.83 | 21 | PR6 |
| 4 | 52 | 0.48 | 0.86 | 21 | PR6 |
| 5 | 50 | 0.46 | 0.85 | 18 | PR6 |
Interfaces
7 interfaces between chains.
- A–B · 1460 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 1456 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 1451 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 256 Ų buried · 4 hydrogen bonds · protein-protein
- B–E · 157 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 covalent (covalent ligand).
Compared structures
- 4LHO · Crystal Structure of FG41Malonate Semialdehyde Decarboxylase inhibited by… · 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 F2Z288
- Elsewhere: RCSB PDB 4LHO · PDBe 4LHO · UniProt F2Z288
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