MolNFT v1 · #15588 · protein
Crystal structure of pichia pastoris lysyl oxidase pplo
1N9E: “Crystal structure of pichia pastoris lysyl oxidase pplo”. X-ray diffraction, 4 ligands (NAG, CA, CU), 20 pockets (best druggability 0.89). MolNFT v1 #15588 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1N9E
- Type
- protein
- Length
- 2,940 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysyl oxidase
- EC
- 1.4.3.13
- Ligands
- NAG, CA, CU, SO4
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 1 distinct chain · 14% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Lysyl oxidase (EC 1.4.3.13) | protein | 735 | 14% helix, 40% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 24 copies · chains A, B, C, D
- CA · Calcium ion · metal · 8 copies · chains A, B, C, D
- CU · Copper (II) ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 28 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, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1103 | 0.89 | 0.90 | 114 | SO4 |
| 2 | 1185 | 0.88 | 0.89 | 120 | SO4 |
| 3 | 1100 | 0.83 | 0.84 | 99 | empty |
| 4 | 116 | 0.78 | 0.97 | 27 | empty |
| 5 | 120 | 0.77 | 0.96 | 30 | empty |
Interfaces
6 interfaces between chains.
- A–B · 8852 Ų buried · 165 hydrogen bonds · protein-protein
- C–D · 8841 Ų buried · 161 hydrogen bonds · protein-protein
- B–C · 252 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 61 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 59 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 20 glycan, 12 disulfide, 4 modified (N-glycosylation, disulfide, nonstandard).
Compared structures
- 1N9E · Crystal structure of Pichia pastoris Lysyl Oxidase PPLO · 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
- Elsewhere: RCSB PDB 1N9E · PDBe 1N9E
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