MolNFT v1 · #30987 · protein
Crystal structure of benzaldehyde lyase (bal)- semet
2AG1: “Crystal structure of benzaldehyde lyase (bal)- semet”. X-ray diffraction, 2 ligands (TPP, MG), 20 pockets (best druggability 0.78). MolNFT v1 #30987 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2AG1
- Type
- protein
- Length
- 2,212 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Benzaldehyde lyase
- EC
- 4.1.2.38
- Ligands
- TPP, MG
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Benzaldehyde lyase (EC 4.1.2.38) | protein | 553 | 45% helix, 17% strand | — |
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, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 621 | 0.78 | 0.84 | 67 | MG, TPP |
| 2 | 595 | 0.78 | 0.84 | 70 | TPP |
| 3 | 219 | 0.77 | 0.92 | 45 | empty |
| 4 | 597 | 0.77 | 0.83 | 67 | MG, TPP |
| 5 | 566 | 0.77 | 0.83 | 65 | MG, TPP |
Interfaces
6 interfaces between chains.
- A–B · 3301 Ų buried · 55 hydrogen bonds · protein-protein
- C–D · 3297 Ų buried · 57 hydrogen bonds · protein-protein
- B–C · 1296 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 1293 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 609 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 44 modified (engineered).
Compared structures
- 2AG1 · Crystal structure of Benzaldehyde lyase (BAL)- SeMet · the same entry in another collection · chain D against D, 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
- Elsewhere: RCSB PDB 2AG1 · PDBe 2AG1
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