Research workbench
Structure of latex clearing protein lcp in the open state with bound imidazole
Analyse Structure of latex clearing protein lcp in the open state with bound imidazole in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5O1L
- Type
- protein
- Length
- 748 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rubber oxygenase
- EC
- 1.13.-.-
- UniProt
- Q3L8N0
- Ligands
- HEM
- Pockets
- 10 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 64% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Rubber oxygenase (EC 1.13.-.-) | protein | 375 | 63% helix, 1% strand | Q3L8N0 |
| B | Rubber oxygenase (EC 1.13.-.-) | protein | 373 | 64% helix, 1% strand | Q3L8N0 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- IMD · Imidazole · additive · 4 copies · chains A, B
- BU3 · (R,R)-2,3-butanediol · additive · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 509 | 0.84 | 0.90 | 57 | HEM, IMD |
| 2 | 446 | 0.83 | 0.90 | 57 | HEM, IMD |
| 3 | 217 | 0.76 | 0.90 | 39 | BU3 |
| 4 | 78 | 0.58 | 0.88 | 18 | BU3 |
| 5 | 70 | 0.43 | 0.80 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 508 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5O1L · Structure of Latex Clearing Protein LCP in the open state with bound imidazole · the same entry in another collection · chain A against A, TM-score 1.00
- Q3L8N0 · AlphaFold monomer V2.0 prediction for rubber oxygenase (Q3L8N0) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 Q3L8N0
- Elsewhere: RCSB PDB 5O1L · PDBe 5O1L · UniProt Q3L8N0
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