Research workbench
Discovery and characterization of a novel thermostable and highly halotolerant GH5 cellulase from an icelandic hot spring isolate
Analyse Discovery and characterization of a novel thermostable and highly halotolerant… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FIP
- Type
- protein
- Length
- 1,322 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GH5 cellulase
- EC
- 3.2.1.4
- Ligands
- CL
- Pockets
- 10 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | GH5 cellulase (EC 3.2.1.4) | protein | 331 | 34% helix, 19% strand | — |
| B | GH5 cellulase (EC 3.2.1.4) | protein | 332 | 34% helix, 19% strand | — |
| D | GH5 cellulase (EC 3.2.1.4) | protein | 328 | 33% helix, 19% strand | — |
Ligands and binding sites
- CL · Chloride ion · ion · 7 copies · chains A, C, B, D
- EDO · 1,2-ethanediol · additive · 18 copies · chains A, B, C, D
- IPA · Isopropyl alcohol · additive · 13 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 11 copies · chains A, C, B, D
- PGE · Triethylene glycol · additive · 4 copies · chains A, C, B
- PG6 · 1-(2-methoxy-ethoxy)-2-{2-[2-(2-methoxy-ethoxy]-ethoxy}-ethane · additive · chains B, D
- PG4 · Tetraethylene glycol · additive · chains B, 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 660 | 0.68 | 0.76 | 91 | EDO, IPA |
| 2 | 374 | 0.65 | 0.79 | 39 | PG6, PG4, IPA |
| 3 | 377 | 0.62 | 0.77 | 32 | PEG, PGE |
| 4 | 166 | 0.46 | 0.75 | 30 | PEG, IPA |
| 5 | 143 | 0.45 | 0.76 | 24 | empty |
Interfaces
5 interfaces between chains.
- B–D · 915 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 868 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 401 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 35 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 18 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5FIP · Discovery and characterization of a novel thermostable and highly halotolerant GH5… · 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
- Elsewhere: RCSB PDB 5FIP · PDBe 5FIP
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