MolNFT v1 · #120625 · protein
Crystal structure of a thermostable lipase from marine streptomyces
5H6G · Putative secreted lipase: “Crystal structure of a thermostable lipase from marine streptomyces”. X-ray diffraction, 3 ligands (K, PO4, CL), 7 pockets (best druggability 0.81). MolNFT v1 #120625 on GenesisL1: 3D structure, binding…
- PDB
- 5H6G
- Type
- protein
- Length
- 760 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative secreted lipase
- UniProt
- H0B8D4
- Ligands
- K, PO4, CL
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Putative secreted lipase | protein | 253 | 38% helix, 15% strand | H0B8D4 |
| B | Putative secreted lipase | protein | 254 | 38% helix, 15% strand | H0B8D4 |
Ligands and binding sites
- K · Potassium ion · metal · chains B
- PO4 · Phosphate ion · ion · 4 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A
- GOL · Glycerol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1018 | 0.81 | 0.82 | 100 | empty |
| 2 | 82 | 0.76 | 0.98 | 28 | empty |
| 3 | 181 | 0.51 | 0.78 | 29 | empty |
| 4 | 66 | 0.51 | 0.85 | 21 | empty |
| 5 | 68 | 0.42 | 0.81 | 17 | empty |
Interfaces
3 interfaces between chains.
- B–C · 944 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 463 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 34 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 5H6G · Crystal structure of a thermostable lipase from Marine Streptomyces · 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 H0B8D4
- Elsewhere: RCSB PDB 5H6G · PDBe 5H6G · UniProt H0B8D4
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