Research workbench
Crystal structure of benzaldehyde lyase in complex with the inhibitor mbp
Analyse Crystal structure of benzaldehyde lyase in complex with the inhibitor mbp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3D7K
- Type
- protein
- Length
- 1,108 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Benzaldehyde lyase
- EC
- 4.1.2.38
- UniProt
- Q9F4L3
- Ligands
- D7K, CA
- Pockets
- 14 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Benzaldehyde lyase (EC 4.1.2.38) | protein | 554 | 43% helix, 17% strand | Q9F4L3 |
Ligands and binding sites
- D7K · 3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-2-{(S)-hydroxy[(R)-hydroxy(methoxy)phosphoryl]phenylmethyl}-5-(2-{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3-thiazol-3-ium · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 843 | 0.77 | 0.80 | 83 | D7K, CA |
| 2 | 731 | 0.74 | 0.80 | 73 | D7K, CA |
| 3 | 58 | 0.71 | 0.98 | 16 | empty |
| 4 | 55 | 0.70 | 0.98 | 17 | empty |
| 5 | 211 | 0.55 | 0.79 | 35 | empty |
Interfaces
1 interface between chains.
- A–B · 3315 Ų buried · 54 hydrogen bonds · protein-protein
Compared structures
- 3D7K · Crystal structure of benzaldehyde lyase in complex with the inhibitor MBP · the same entry in another collection · chain B against B, 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 3D7K · PDBe 3D7K · UniProt Q9F4L3
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