MolNFT v1 · #98716 · protein
Crystal structure of native FG41MALONATE semialdehyde decarboxylase
4LHP · FG41 malonate semialdehyde decarboxylase: “Crystal structure of native FG41MALONATE semialdehyde decarboxylase”. X-ray diffraction, 2 ligands (PO4, SO4), 10 pockets (best druggability 0.60). MolNFT v1 #98716 on GenesisL1: 3D…
- PDB
- 4LHP
- Type
- protein
- Length
- 1,570 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- FG41 malonate semialdehyde decarboxylase
- EC
- 4.1.1.-
- UniProt
- F2Z288
- Ligands
- PO4, SO4
- Pockets
- 10 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, G, H, I, J, L | FG41 malonate semialdehyde decarboxylase (EC 4.1.1.-) | protein | 131 | 36% helix, 28% strand | F2Z288 |
| F, K | FG41 malonate semialdehyde decarboxylase (EC 4.1.1.-) | protein | 130 | 38% helix, 28% strand | F2Z288 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- SO4 · Sulfate ion · ion · 2 copies · chains D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 411 | 0.60 | 0.76 | 65 | empty |
| 2 | 195 | 0.53 | 0.78 | 20 | empty |
| 3 | 195 | 0.50 | 0.77 | 19 | empty |
| 4 | 178 | 0.48 | 0.76 | 20 | empty |
| 5 | 176 | 0.48 | 0.76 | 21 | empty |
Interfaces
17 interfaces between chains.
- B–C · 1486 Ų buried · 21 hydrogen bonds · protein-protein
- D–E · 1473 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1473 Ų buried · 19 hydrogen bonds · protein-protein
- J–L · 1463 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 1459 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 4LHP · Crystal Structure of Native FG41Malonate Semialdehyde Decarboxylase · 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 4LHP · PDBe 4LHP · UniProt F2Z288
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