MolNFT v1 · #141413 · protein
The crystal structure of an agarase, AGWH50C
5Z6P · B-agarase: “The crystal structure of an agarase, AGWH50C”. X-ray diffraction, 12 pockets (best druggability 0.72). MolNFT v1 #141413 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5Z6P
- Type
- protein
- Length
- 1,348 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- B-agarase
- UniProt
- A0A023LLI1
- Pockets
- 12 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | B-agarase | protein | 702 | 28% helix, 26% strand | A0A023LLI1 |
| B | B-agarase | protein | 646 | 27% helix, 26% strand | A0A023LLI1 |
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 825 | 0.72 | 0.77 | 74 | empty |
| 2 | 640 | 0.69 | 0.77 | 58 | empty |
| 3 | 436 | 0.68 | 0.80 | 54 | empty |
| 4 | 222 | 0.67 | 0.85 | 39 | empty |
| 5 | 335 | 0.66 | 0.81 | 39 | empty |
Interfaces
1 interface between chains.
- A–B · 391 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5Z6P · The crystal structure of an agarase, AgWH50C · 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 A0A023LLI1
- Elsewhere: RCSB PDB 5Z6P · PDBe 5Z6P · UniProt A0A023LLI1
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