Research workbench
Complete structure of manganese lipoxygenase of gaeumannomyces graminis and partial structure of zonadhesin of komagataella pastoris
Analyse Complete structure of manganese lipoxygenase of gaeumannomyces graminis and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FX8
- Type
- protein
- Length
- 1,428 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Linoleate 11-lipoxygenase; Zonadhesin
- EC
- 1.13.11.12
- UniProt
- Q8X151, F2QXM5
- Ligands
- NAG, MN
- Pockets
- 14 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Linoleate 11-lipoxygenase (EC 1.13.11.12) | protein | 563 | 51% helix, 6% strand | Q8X151 |
| B | Linoleate 11-lipoxygenase (EC 1.13.11.12) | protein | 556 | 51% helix, 6% strand | Q8X151 |
| U | Zonadhesin | protein | 309 | 2% helix, 52% strand | F2QXM5 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 16 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 163 | 0.82 | 0.97 | 29 | empty |
| 2 | 957 | 0.81 | 0.82 | 92 | NAG |
| 3 | 552 | 0.68 | 0.78 | 53 | empty |
| 4 | 310 | 0.63 | 0.80 | 39 | empty |
| 5 | 334 | 0.62 | 0.78 | 37 | empty |
Interfaces
2 interfaces between chains.
- A–B · 866 Ų buried · 2 hydrogen bonds · protein-protein
- A–U · 726 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 glycan, 1 disulfide (N-glycosylation, disulfide).
Compared structures
- 5FX8 · Complete structure of manganese lipoxygenase of Gaeumannomyces graminis and partial… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8X151 · AlphaFold monomer V2.0 prediction for manganese lipoxygenase (Q8X151) · a predicted model of the same protein · chain B against A, TM-score 1.00
- F2QXM5 · AlphaFold monomer V2.0 prediction for putative adhesin (F2QXM5) · a predicted model of the same protein · chain U against A, TM-score 0.99
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 Q8X151
- Every structure of UniProt F2QXM5
- Elsewhere: RCSB PDB 5FX8 · PDBe 5FX8 · UniProt Q8X151 · UniProt F2QXM5
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