MolNFT v1 · #61815 · protein
Leishmania major coproporphyrinogen III oxidase with bound ligand
3DWS: “Leishmania major coproporphyrinogen III oxidase with bound ligand”. X-ray diffraction, 1 ligand (FIC), 8 pockets (best druggability 0.84). MolNFT v1 #61815 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3DWS
- Type
- protein
- Length
- 606 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coproporphyrinogen III oxidase
- EC
- 1.3.3.3
- UniProt
- P84155
- Ligands
- FIC
- Pockets
- 8 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Coproporphyrinogen III oxidase (EC 1.3.3.3) | protein | 302 | 44% helix, 26% strand | P84155 |
| B | Coproporphyrinogen III oxidase (EC 1.3.3.3) | protein | 304 | 45% helix, 26% strand | P84155 |
Ligands and binding sites
- FIC · 5-fluoroindole-2-carboxylic acid · ligand · 2 copies · chains A, B
- ACT · Acetate ion · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 708 | 0.84 | 0.88 | 64 | ACT, FIC |
| 2 | 738 | 0.83 | 0.87 | 62 | ACT, FIC |
| 3 | 171 | 0.46 | 0.75 | 29 | empty |
| 4 | 79 | 0.38 | 0.77 | 18 | empty |
| 5 | 64 | 0.37 | 0.78 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1365 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (engineered).
Compared structures
- 3DWS · Leishmania major Coproporphyrinogen III Oxidase with bound ligand · the same entry in another collection · chain A against A, TM-score 1.00
- P84155 · AlphaFold monomer V2.0 prediction for oxygen-dependent coproporphyrinogen-III oxidase… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P84155
- Elsewhere: RCSB PDB 3DWS · PDBe 3DWS · UniProt P84155
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