Research workbench
Omci in complex with leukotriene B4
Analyse Omci in complex with leukotriene B4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZUO
- Type
- protein
- Length
- 579 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Complement inhibitor
- UniProt
- Q5YD59
- Ligands
- LTB
- Pockets
- 11 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Complement inhibitor | protein | 142 | 18% helix, 44% strand | Q5YD59 |
| B | Complement inhibitor | protein | 145 | 17% helix, 45% strand | Q5YD59 |
| C, D | Complement inhibitor | protein | 146 | 17% helix, 45% strand | Q5YD59 |
Ligands and binding sites
- LTB · Leukotriene B4 · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 561 | 0.75 | 0.82 | 76 | LTB |
| 2 | 220 | 0.75 | 0.89 | 40 | LTB |
| 3 | 184 | 0.74 | 0.90 | 36 | LTB |
| 4 | 392 | 0.72 | 0.83 | 59 | LTB |
| 5 | 203 | 0.55 | 0.79 | 33 | empty |
Interfaces
6 interfaces between chains.
- C–D · 834 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 743 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 382 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 347 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 111 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 3ZUO · OMCI in complex with leukotriene B4 · 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
- Every structure of UniProt Q5YD59
- Elsewhere: RCSB PDB 3ZUO · PDBe 3ZUO · UniProt Q5YD59
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