Research workbench
Crystal structure of benzaldehyde lyase (bal)- native
Analyse Crystal structure of benzaldehyde lyase (bal)- native in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2AG0
- 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
- Ligands
- TPP, MG
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Benzaldehyde lyase (EC 4.1.2.38) | protein | 554 | 46% 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, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 407 | 0.81 | 0.89 | 75 | empty |
| 2 | 385 | 0.80 | 0.89 | 73 | empty |
| 3 | 527 | 0.79 | 0.86 | 61 | MG, TPP |
| 4 | 371 | 0.79 | 0.88 | 54 | TPP |
| 5 | 126 | 0.79 | 0.97 | 44 | empty |
Interfaces
6 interfaces between chains.
- A–B · 3375 Ų buried · 52 hydrogen bonds · protein-protein
- C–D · 3371 Ų buried · 52 hydrogen bonds · protein-protein
- B–C · 1297 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 1289 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 564 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 2AG0 · Crystal structure of Benzaldehyde lyase (BAL)- native · 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 2AG0 · PDBe 2AG0
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