MolNFT v1 · #119476 · protein
Complete structure of manganese lipoxygenase of gaeumannomyces graminis and partial structure of zonadhesin of komagataella pastoris
5FX8 · Linoleate 11-lipoxygenase: “Complete structure of manganese lipoxygenase of gaeumannomyces graminis and partial structure of zonadhesin…”. X-ray diffraction, 2 ligands (NAG, MN), 14 pockets (best druggability 0.82). MolNFT v1…
- 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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