Research workbench
Substrate protein interactions in the limbus region of the catalytic site of candida antarctica lipase B
Analyse Substrate protein interactions in the limbus region of the catalytic site of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TP8
- Type
- protein
- Length
- 951 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lipase B
- EC
- 3.1.1.3
- UniProt
- P41365
- Ligands
- DEP, NTK, NAG
- Pockets
- 5 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Lipase B (EC 3.1.1.3) | protein | 317 | 38% helix, 16% strand | P41365 |
Ligands and binding sites
- DEP · Diethyl phosphonate · ligand · 3 copies · chains A, B, C
- NTK · 2,3-di(butanoyloxy)propyl butanoate · ligand · 2 copies · chains A, B, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 632 | 0.87 | 0.92 | 63 | DEP, NTK |
| 2 | 177 | 0.59 | 0.82 | 27 | DEP |
| 3 | 443 | 0.54 | 0.72 | 39 | empty |
| 4 | 109 | 0.43 | 0.77 | 20 | empty |
| 5 | 125 | 0.42 | 0.75 | 19 | empty |
Interfaces
2 interfaces between chains.
- A–B · 826 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 61 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 3 covalent, 3 glycan (disulfide, covalent ligand, N-glycosylation).
Compared structures
- 6TP8 · Substrate protein interactions in the limbus region of the catalytic site of Candida… · the same entry in another collection · chain A against A, TM-score 1.00
- P41365 · AlphaFold monomer V2.0 prediction for lipase B (P41365) · a predicted model of the same protein · 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 P41365
- Elsewhere: RCSB PDB 6TP8 · PDBe 6TP8 · UniProt P41365
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