Research workbench
Hyperthermophilic GH6 cellobiohydrolase II (HMCEL6A) in complex with trisaccharide
Analyse Hyperthermophilic GH6 cellobiohydrolase II (HMCEL6A) in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6K54
- Type
- protein
- Length
- 1,284 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GH6 cellobiohydrolase, HMCEL6A
- EC
- 3.2.1.91
- Ligands
- BGC, GLC, CA
- Pockets
- 9 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | GH6 cellobiohydrolase, HMCEL6A (EC 3.2.1.91) | protein | 428 | 35% helix, 13% strand | — |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 12 copies · chains A, B, C
- GLC · alpha-D-glucopyranose · sugar · chains A
- CA · Calcium ion · metal · 7 copies · chains A, B, C
- IMD · Imidazole · additive · 6 copies · chains A, B, C
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, C
- PGE · Triethylene glycol · additive · 2 copies · chains A, B
- PE4 · 2-{2-[2-(2-{2-[2-(2-ethoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-ethanol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 998 | 0.82 | 0.83 | 109 | CA, IMD |
| 2 | 802 | 0.80 | 0.83 | 73 | BGC |
| 3 | 894 | 0.79 | 0.82 | 95 | BGC |
| 4 | 600 | 0.77 | 0.84 | 64 | GLC, BGC |
| 5 | 451 | 0.67 | 0.79 | 58 | IMD |
Interfaces
2 interfaces between chains.
- A–C · 926 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 631 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide (disulfide).
Compared structures
- 6K54 · Hyperthermophilic GH6 cellobiohydrolase II (HmCel6A) in complex with trisaccharide · 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 6K54 · PDBe 6K54
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