Research workbench
Crystal structure of the laminarinase catalytic domain from thermotoga maritima MSB8 in complex with gluconolactone
Analyse Crystal structure of the laminarinase catalytic domain from thermotoga maritima… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3AZZ
- Type
- protein
- Length
- 1,000 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Laminarinase
- EC
- 3.2.1.39
- UniProt
- Q9WXN1
- Ligands
- LGC, CA, SO4
- Pockets
- 10 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 7% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Laminarinase (EC 3.2.1.39) | protein | 250 | 7% helix, 49% strand | Q9WXN1 |
Ligands and binding sites
- LGC · D-glucono-1,5-lactone · ligand · 3 copies · chains A, B, C
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 743 | 0.67 | 0.75 | 74 | empty |
| 2 | 565 | 0.63 | 0.75 | 50 | SO4 |
| 3 | 286 | 0.62 | 0.80 | 35 | LGC |
| 4 | 295 | 0.62 | 0.79 | 37 | LGC |
| 5 | 283 | 0.62 | 0.80 | 37 | empty |
Interfaces
5 interfaces between chains.
- B–C · 466 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 465 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 459 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 410 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 299 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3AZZ · Crystal structure of the laminarinase catalytic domain from Thermotoga maritima MSB8 in… · 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 Q9WXN1
- Elsewhere: RCSB PDB 3AZZ · PDBe 3AZZ · UniProt Q9WXN1
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