MolNFT v1 · #58326 · protein
Crystal structure of the laminarinase catalytic domain from thermotoga maritima MSB8
3B01: “Crystal structure of the laminarinase catalytic domain from thermotoga maritima MSB8”. X-ray diffraction, 3 ligands (CA, SO4, CL), 9 pockets (best druggability 0.66). MolNFT v1 #58326 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3B01
- Type
- protein
- Length
- 1,003 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
- CA, SO4, CL
- Pockets
- 9 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Laminarinase (EC 3.2.1.39) | protein | 251 | 7% helix, 47% strand | Q9WXN1 |
| B | Laminarinase (EC 3.2.1.39) | protein | 250 | 7% helix, 49% strand | Q9WXN1 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, D, C
- CL · Chloride ion · ion · 3 copies · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 691 | 0.66 | 0.75 | 63 | empty |
| 2 | 281 | 0.64 | 0.81 | 34 | empty |
| 3 | 226 | 0.63 | 0.82 | 33 | empty |
| 4 | 305 | 0.63 | 0.79 | 33 | empty |
| 5 | 522 | 0.62 | 0.75 | 55 | SO4 |
Interfaces
5 interfaces between chains.
- C–D · 475 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 465 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 449 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 405 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 298 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3B01 · Crystal structure of the laminarinase catalytic domain from Thermotoga maritima MSB8 · 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 3B01 · PDBe 3B01 · UniProt Q9WXN1
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