Research workbench
Structure of PFGH50B
Analyse Structure of PFGH50B in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XJ9
- Type
- protein
- Length
- 1,387 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Agarase
- UniProt
- A0A5B0UCF9
- Pockets
- 10 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Agarase | protein | 706 | 28% helix, 24% strand | A0A5B0UCF9 |
| B | Agarase | protein | 681 | 28% helix, 24% strand | A0A5B0UCF9 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 358 | 0.76 | 0.87 | 54 | empty |
| 2 | 261 | 0.71 | 0.86 | 49 | empty |
| 3 | 199 | 0.70 | 0.87 | 42 | empty |
| 4 | 533 | 0.62 | 0.74 | 63 | EDO |
| 5 | 455 | 0.60 | 0.75 | 43 | empty |
Interfaces
1 interface between chains.
- A–B · 674 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6XJ9 · Structure of PfGH50B · 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 A0A5B0UCF9
- Elsewhere: RCSB PDB 6XJ9 · PDBe 6XJ9 · UniProt A0A5B0UCF9
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