MolNFT v1 · #67098 · protein
Structure of benzaldehyde lyase A28S mutant with monomethyl benzoylphosphonate
3IAF: “Structure of benzaldehyde lyase A28S mutant with monomethyl benzoylphosphonate”. X-ray diffraction, 2 ligands (TPP, MG), 20 pockets (best druggability 0.78). MolNFT v1 #67098 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 3IAF
- Type
- protein
- Length
- 2,216 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Benzaldehyde lyase
- EC
- 4.1.2.38
- UniProt
- Q9F4L3
- Ligands
- TPP, MG
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Benzaldehyde lyase (EC 4.1.2.38) | protein | 554 | 42% helix, 18% strand | Q9F4L3 |
Ligands and binding sites
- TPP · Thiamine diphosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 228 | 0.78 | 0.92 | 51 | empty |
| 2 | 588 | 0.77 | 0.83 | 68 | TPP, MG |
| 3 | 699 | 0.77 | 0.82 | 77 | TPP, MG |
| 4 | 663 | 0.76 | 0.81 | 82 | TPP |
| 5 | 709 | 0.76 | 0.81 | 91 | TPP, MG |
Interfaces
6 interfaces between chains.
- C–D · 3365 Ų buried · 55 hydrogen bonds · protein-protein
- A–B · 3363 Ų buried · 52 hydrogen bonds · protein-protein
- B–C · 1348 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 1286 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 574 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (phosphorylation).
Compared structures
- 3IAF · Structure of benzaldehyde lyase A28S mutant with monomethyl benzoylphosphonate · 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 Q9F4L3
- Elsewhere: RCSB PDB 3IAF · PDBe 3IAF · UniProt Q9F4L3
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