MolNFT v1 · #58325 · protein
Crystal structure of the laminarinase catalytic domain from thermotoga maritima MSB8 in complex with cetyltrimethylammonium bromide
3B00: “Crystal structure of the laminarinase catalytic domain from thermotoga maritima MSB8 in complex with…”. X-ray diffraction, 2 ligands (16A, CA), 9 pockets (best druggability 0.66). MolNFT v1 #58325 on GenesisL1: 3D structure, binding…
- PDB
- 3B00
- Type
- protein
- Length
- 1,004 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
- 16A, CA
- Pockets
- 9 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 8% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Laminarinase (EC 3.2.1.39) | protein | 251 | 8% helix, 48% strand | Q9WXN1 |
Ligands and binding sites
- 16A · Cetyl-trimethyl-ammonium · ligand · 3 copies · chains A, B, D
- CA · Calcium 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
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 | 627 | 0.66 | 0.76 | 60 | empty |
| 2 | 321 | 0.65 | 0.80 | 41 | 16A |
| 3 | 282 | 0.64 | 0.81 | 36 | 16A |
| 4 | 604 | 0.64 | 0.75 | 57 | empty |
| 5 | 578 | 0.64 | 0.75 | 57 | empty |
Interfaces
5 interfaces between chains.
- C–D · 481 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 471 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 449 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 417 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 295 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3B00 · Crystal structure of the laminarinase catalytic domain from Thermotoga maritima MSB8 in… · 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
- Every structure of UniProt Q9WXN1
- Elsewhere: RCSB PDB 3B00 · PDBe 3B00 · UniProt Q9WXN1
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