Research workbench
Structure of CpGH84A
Analyse Structure of CpGH84A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PV4
- Type
- protein
- Length
- 2,406 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.2
- Source
- Clostridium perfringens ATCC 13124
- Molecule
- Glycoside Hydrolase
- EC
- 3.2.1.35
- UniProt
- A0A0H2YRL1
- Ligands
- CA
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · resolution 2.2 · 4 distinct chains · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycoside Hydrolase (EC 3.2.1.35) | protein | 589 | 42% helix, 16% strand | A0A0H2YRL1 |
| B | Glycoside Hydrolase (EC 3.2.1.35) | protein | 607 | 43% helix, 15% strand | A0A0H2YRL1 |
| C | Glycoside Hydrolase (EC 3.2.1.35) | protein | 608 | 43% helix, 16% strand | A0A0H2YRL1 |
| D | Glycoside Hydrolase (EC 3.2.1.35) | protein | 602 | 43% helix, 16% strand | A0A0H2YRL1 |
Ligands and binding sites
- CA · Calcium ion · metal · 19 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 23 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1126 | 0.86 | 0.87 | 132 | EDO |
| 2 | 994 | 0.85 | 0.86 | 103 | EDO |
| 3 | 287 | 0.69 | 0.84 | 42 | empty |
| 4 | 523 | 0.62 | 0.75 | 49 | empty |
| 5 | 482 | 0.59 | 0.75 | 52 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1213 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1213 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 311 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 284 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 170 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6PV4 · Structure of CPGH84A · 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 A0A0H2YRL1
- Elsewhere: RCSB PDB 6PV4 · PDBe 6PV4 · UniProt A0A0H2YRL1
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